Predicted mutation
evidence seq id position mutation freq annotation gene description
RA REL606 1,144,610 C→T 19.7% A31T (GCA→ACA)  flgM ← anti‑sigma factor for FliA (sigma 28)

Read alignment evidence...
  seq id position change freq score reads annotation genes product
*REL6061,144,6100C→T19.7% 2.3 ‑4.2 0.02591flgManti‑sigma factor for FliA (sigma 28)
Reads supporting (aligned to +/- strand):  new base (5/0):  ref base (7/13):  total (12/13)
Fisher's exact test strand distribution p-value = 1.49e-02
Kolmogorov-Smirnov test that lower quality scores support polymorphism than reference p-value = 1.00e+00

TCACACTGGTGCTGGTGGAGGCGGTTGTTTTTGCCGCCCGGCTGTTCGTTACCGGCGCGTCAGTGGTTT  >  REL606/1144577‑1144645
                                 |                                   
tCACACTGGTGCTGGTGGAGGCGGTTGTTTTTgccg                                   <  1:6612119/36‑1 (MQ=255)
  acacTGGTGCTGGTGGAGGCGGTTGTTTTTgccgcc                                 <  1:7359714/36‑1 (MQ=255)
   cacTGGTGCTGGTGGAGGCGGTTGTTTTTTTCGccc                                >  1:5142860/1‑36 (MQ=37)
      tggtgctggtgGAGGCGGTTGTTTTTGCCGCCCGGc                             <  1:5450404/36‑1 (MQ=255)
       gttgctggtgGGGGCGGTTGTTTTTGCCGCCCGGCt                            <  1:2384426/34‑1 (MQ=38)
        gtgctggtgGAGGCGGTTTTTTTTTTCGCCCGGCTg                           >  1:7771085/1‑36 (MQ=25)
         tgctggtgGAGGCGGTTGTTTTTTTTGCCCGGCTGt                          >  1:6128786/1‑36 (MQ=25)
         tgctggtgGAGGCGGTTGTTTTTGCCGCCCGGCTGt                          <  1:2462796/36‑1 (MQ=255)
         tgctggtgGAGGCGGTTGTTTTTGCCGCCCGGCTGt                          <  1:3752633/36‑1 (MQ=255)
          gctggtgGAGGCGGTTGTTTTTGCCGCCCGGCTGtt                         <  1:6149016/36‑1 (MQ=255)
          gctggtgGAGGCGGTTGTTTTTGCCGCCCGGCTGtt                         <  1:2379753/36‑1 (MQ=255)
           ctggtgGAGGCGGTTGTTTTTGCCGCCCGGCTGTTc                        <  1:2807474/36‑1 (MQ=255)
            tggtggAGGCGGTTTTTTTTTTCGCCCCGCTGtttt                       >  1:6753910/1‑34 (MQ=16)
             ggtggAGGCGGTTTTTTTTTTCGCCCGGCTGttttt                      >  1:5592354/1‑33 (MQ=16)
                ggAGGCGGTTGTTTTTGCCGCCCGGCTGTTCGTTAc                   <  1:3450572/36‑1 (MQ=255)
                   ggCGGTTGTTTTTGCCGCCCGGCTGTTCGTTACCgg                <  1:807683/36‑1 (MQ=255)
                    gCGGTTGTTTTTGCCGCCCGGCTGTTCGTTACCGgc               >  1:3697313/1‑36 (MQ=255)
                    gCGGTTGTTTTTGCCGCCCGGCTGTTCGTTACCGgc               <  1:254803/36‑1 (MQ=255)
                    gCGGTTGTTTTTGCCGCCCGGCTGTTCGTTACCGgc               <  1:623136/36‑1 (MQ=255)
                      ggTTGTTTTTGCCGCCCGGCTGTTCGTTACCGgcgg             >  1:3925253/1‑35 (MQ=255)
                       gttgttTTTGCCGCCCGGCTGTTCGTTACCGGcgcg            >  1:3928836/1‑36 (MQ=255)
                       gttgttTTTGCCGCCCGGCTGTTCGTTACCGGcgcg            <  1:356639/36‑1 (MQ=255)
                          gttTTTGCCGCCCGGCTGTTCGTTACCGGCGCGTCa         >  1:1482655/1‑36 (MQ=255)
                           tttttGCCGCCCGGCTGTTCGTTACCGGCGCGTCAg        >  1:6596408/1‑36 (MQ=255)
                            ttttGCCGCCCGGCTGTTCGTTACCGGCGCGTCAGt       >  1:3713893/1‑36 (MQ=255)
                              ttGCCGCCCGGCTGTTCGTTACCGGCGCGTCAGTgg     >  1:5213954/1‑36 (MQ=255)
                               tGCCGCCCGCCTGTTCGTTACCGGCGCGTCAGTGGt    <  1:227908/36‑1 (MQ=255)
                                 ccgccCGGCTGTTCGTTACCGGCGCGTCAGTGGttt  <  1:4256094/36‑1 (MQ=255)
                                 |                                   
TCACACTGGTGCTGGTGGAGGCGGTTGTTTTTGCCGCCCGGCTGTTCGTTACCGGCGCGTCAGTGGTTT  >  REL606/1144577‑1144645

Base quality scores:  ATCG  < 3 ≤  ATCG  < 7 ≤  ATCG  < 19 ≤  ATCG  < 30 ≤  ATCG  < 37 ≤  ATCG