Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A2 F13 I0 R1 203 85.6 3649704 98.8% 3605907 146.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947_CJ‑RC 3,171,774 A→T 20.9% I16F (ATT→TTT)  PP_2784 → short‑chain dehydrogenase/reductase family oxidoreductase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_002947_CJ‑RC3,171,7740AT20.9% 78.0 / 6.2 45I16F (ATT→TTT) PP_2784short‑chain dehydrogenase/reductase family oxidoreductase
Reads supporting (aligned to +/- strand):  ref base A (27/7);  new base T (5/5);  total (32/13)
Fisher's exact test for biased strand distribution p-value = 1.05e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCCCGGCCTGAAGAAATTGCCGACGCGGTGCTGTATCTGGCCGAGCGCGGCCTGTACATCACGGGCGAAGTCCTGTCCGTCAACGGCGGATTGAAAATGCCATGAGCCAGTTACGCACGATTGTGATTACCGGCGC‑GGCCAATGGTATTGG‑CCGCGCCGTCGC‑GGAAAGTTTTGCAGCCCAGGCCGAGCACCTTTTGATCTTGCTTGATCGGGATCTGGCAACCTTGCAGGGGTGGGTCACCGAGGGCGAATTTGCCGCTCGTATCGAAACCCATCAAGCGAACATCGCCGAT  >  NC_002947_CJ‑RC/3171628‑3171920
                                                                                                                                                   |                                                                                                                                                    
gcgaggCCTGAAGAAATTGCCGACGCGGTGCTGTATCTGGCCGAGCGCGGCCTGTACATCACGGGCGAAGTCCTGTCCGTCAACGGCGGATTGAAAATGCCATGAGCCAGTTACGCACGATTGTGATTACCGGCGC‑GGCCAATGGTAtt                                                                                                                                                    <  5:113547/145‑1 (MQ=255)
gCCCGGCCTGAAGAAATTGCCGACGCGGTGCTGTATCTGGCCGAGCGCGGCCTGTACATCACGGGCGAAGTCCTGTCCGTCAACGGCGGATTGAAAATGCCATGAGCCAGTTACGCACGATTGTGATTACCGGCGC‑GGCCAATGGTAtt                                                                                                                                                    <  8:354443/149‑1 (MQ=255)
gCCCGGCCTGAAGAAATTGCCGACGCGGTGCTGTATCTGGCCGAGCGCGGCCTGTACATCACGGGCGAAGTCCTGTCCGTCAACGGCGGATTGAAAATGCCATGAGCCAGTTACGCACGATTGTGATTACCGGCGC‑GGCCAATGGTAtt                                                                                                                                                    <  3:106700/149‑1 (MQ=255)
       cTGAAGAAATTGCCGACGCGGTGCTGTATCTGGCCGAGCGCGGCCTGTACATCACGGGCGAAGTCCTGTCCGTCAACGGCGGATTGAAAATGCCATGAGCCAGTTACGCACGATTGTGATTACCGGCGC‑GGCCAATGGTTTTGG‑Gcgcg                                                                                                                                            >  3:348783/1‑149 (MQ=255)
       cTGAAGAAATTGCCGACGCGGTGCTGTATCTGGCCGAGCGCGGCCTGTACATCACGGGCGAAGTCCTGTCCGTCAACGGCGGATTGAAAATGCCATGAGCCAGTTACGCACGATTGTGATTACCGGCGC‑GGCCAATGGTATTGG‑Ccgcg                                                                                                                                            >  5:317236/1‑149 (MQ=255)
        tGAAGAAATTGCCGACGCGGTGCTGTATCTGGCCGAGCGCGGCCTGTACATCACGGGCGAAGTCCTGTCCGTCAACGGCGGATTGAAAATGCCATGAGCCAGTTACGCACGATTGTGATTACCGGCGC‑GGCCAATGGTATTGG‑CCgcgc                                                                                                                                           >  2:147856/1‑149 (MQ=255)
         gaagaaATTGCCGACGCGGTGCTGTATCTGGCCGAGCGCGGCCTGTACATCACGGGCGAAGTCCTGTCCGTCAACGGCGGATTGAAAATGCCATGAGCCAGTTACGCACGATTGTGATTACCGGCGC‑GGCCAATGGTATTGG‑CCGCGcc                                                                                                                                          >  7:45805/1‑149 (MQ=255)
         gaagaaATTGCAGACGCGGTGCTGTATCTGGCCGAGCGCGGCCTGTACATCACGGGCGAAGTCCTGTCCGTCAACGGCGGATTGAAAATGCCATGAGCCAGTTACGCACGATTGTGATTACCGGCGC‑GGGAAATGGTATTTG‑caccccc                                                                                                                                          >  1:155176/1‑143 (MQ=255)
          aagaaATTGCCGACGCGGTGCTGTATCTGGCCGAGCGCGGCCTGTACATCACGGGCGAAGTCCTGTCCGTCAACGGCGGATTGAAAATGCCATGAGCCAGTTACGCACGATTGTGATTACCGGCGC‑GGCCAATGGTATTGG‑CCgcgc                                                                                                                                           <  6:442961/147‑1 (MQ=255)
            gaaATTGCCGACGCGGTGCTGTATCTGGCCGAGCGCGGCCTGTACATCACGGGCGAAGTCCTGTCCGTCAACGGCGGATTGAAAATGCCATGAGCCAGTTACGCACGATTGTGATTACCGGCGC‑GGCCAATGGTATTGG‑CCGCGCCGTc                                                                                                                                       >  3:228880/1‑149 (MQ=255)
              aaTTGCCGACGCGGTGCTGTATCTGGCCGCGCGCGGCCTGTACATCACGGGCGATGTCCTGCCCGTCACCGGCTTATTTAAAATGCCATGAGCCATTTACGCACTTTTGTTATTCCCGGCGC‑GGCCAATTGTTTTGG‑CCCCGCCGTcgc                                                                                                                                     <  2:155545/149‑1 (MQ=255)
                   ccGACGCGGTGCTGTATCTGGCCGAGCGCGGCCTGTACATCACGGGCGAAGTCCTGTCCGTCAACGGCGGATTGAAAATGCCATGAGCCAGTTACGCACGATTGTGATTACCGGCGC‑GGCCAATGGTATTGG‑CCGCGCCGTCGC‑GGa                                                                                                                                 >  2:8174/1‑147 (MQ=255)
                     gACGCGGTGCTGTATCTGGCCGAGCGCGGCCTGTACATCACGGGCGAAGTCCTGTCCGTCAACGGCGGATTGAAAATGCCATGAGCCAGTTACGCACGATTGTGATTACCGGCGC‑GGGCAATTGTATTGG‑CCGCGCCGGGGC‑GGGAAGt                                                                                                                             >  3:363243/1‑149 (MQ=255)
                     gACGCGGTGCTGTATCTGGCCGAGCGCGGCCTGTACATCACGGGCGAAGTCCTGTCCGTCAACGGCGGATTGAAAATGCCATGAGCCAGTTACGCACGATTGTGATTACCGGCGC‑GGCCAAAGGGAATGG‑CCGCCCCGTCGC‑GGAAAGt                                                                                                                             >  4:124525/1‑149 (MQ=255)
                              cTGTATCTGGCCGAGCGCGGCCTGTACATCACGGGCGAAGTCCTGTCCGTCAACGGCGGATTGAAAATGCCATGAGCCAGTTACGCGCGATTGTGATTACCGGCGC‑GGCCAATGGTATTGG‑CCGCGCCGTCGC‑GGAAAGTTTTGCAGcc                                                                                                                    >  4:186060/1‑149 (MQ=255)
                                       gCCGAGCGCGGCCTGTACATCACGGGCGAAGTCCTGTCCGTCAACGGCGGATTGAAAATGCCATGAGCCAGTTACGCACGATTGTGATTACCGGGGC‑CGCCCAATGTTTTTG‑CCCCGCCGGGGCGGGAATATTTTGAAGACCAGGcccg                                                                                                            >  1:224718/1‑147 (MQ=255)
                                         cGAGCGCGGCCTGTACATCACGGGCGAAGTCCTGTCCGTCAACGGCGGATTGAAAATGCCATGAGCCAGTTACGCACGATTGTGATTACCGGCGCGGGCCATTGGTTTTGG‑‑CGCGCCGTGGC‑GGGTATTTTTTGAGCgccggccgcgga                                                                                                         >  1:205448/1‑145 (MQ=255)
                                         cGAGCGCGGCCTGTACATCACGGGCGAAGTCCTGTCCGTCAACGGCGGATTGAAAATGCCATGAGCCAGTTACGCACGATTGTGATTACCGGCGC‑GGCCAATGGTATTGG‑CCGCGCCGTCGC‑GGAAAGTTTTGCAGCCCAGGCCGAGCa                                                                                                         >  8:279734/1‑149 (MQ=255)
                                         cGAGCGCGGCCTGTACATCACGGGCGAAGTCCTGTCCGTCAACGGCGGATTGAAAATGCCATGAGCCAGTTACGCACGATTGTGATTACCGGCGC‑GGCCAATGGTATTGG‑CCGCGCCGGCGC‑CGCAAGTTTTGCATCCCCGGCCGAGcc                                                                                                         >  6:133625/1‑148 (MQ=255)
                                                              gggCGAAGTCCTGTCCGTCAACGGCGGATTGAAAATGCCATGAGCCAGTTACGCACGATTGTGATTACCGGCGC‑GGCCAAAGGTATTGG‑CCGCGCCGTCGC‑GGTAAGTTTTGCAGCCCAGGCCCAGCACCTTTTGATATTGGTTGTTCg                                                                                    >  2:157535/1‑149 (MQ=255)
                                                                 cGAAGTCCTGTCCGTCAACGGCGGATTGAAAATGCCATGAGCCAGTTACGCACGATTGTGATTACCGGCGC‑GGCCAATGGTATTTG‑CCGCGCCGTCGC‑GGAAATTTTTTCAGCCCACGCCGAGCACCATTTTATATTTCTTGATAGGGa                                                                                 >  3:360254/1‑149 (MQ=255)
                                                                  gAAGTCCTGTCCGTCAACGGCGGATTGAAAATGCCATGAGCCAGTTACGCACGATTGTGATTACCGGCGC‑GGCCAATGGTATTGG‑CCGCGCCGTCGC‑GGAAAGTTTTGCAGCCCAGGCCGAGCACCTTTTGATCTTGCTTGATCGGGa                                                                                 >  6:416218/1‑148 (MQ=255)
                                                                  gAAGTCCTGTCCGTCAACGGCGGATTGAAAATGCCATGAGCCAGTTACGCACGATTGTGATTACCGGCGC‑GGCCAAAGGTATTGG‑CCGCGCCCGCGC‑GGAAAGTTTTGCAGCCCAGGCCGAGCCCCGTTTGATCATGCGTGATCCGGAt                                                                                >  7:225937/1‑149 (MQ=255)
                                                                     gTCCTGTCCGTCAACGGCGGATTGAAAATGCCATGAGCCAGTTACGCACGATTGTGATTACCGGCGC‑GGCCAATGGTATTGG‑CCACGCCGTCGC‑GGAAAGTTTTGCAGCCCAGGCCGAGCACCTTTTGATCTTGCTTGATCGGGATCTg                                                                             <  7:445306/149‑1 (MQ=255)
                                                                        cTGTCCGTCAACGGCGGATTGAAAATGCCATGAGCCAGTTACGCACGATTGTGATTACCGGCGC‑GGCCAATGGTTTTGG‑CCGCGCCCTGGC‑GGAAAGTTTTGCCGCCCAGGCCGAGCCCCTGTTTTTCTTGCTTGATAGGGGTCTGGc                                                                           >  5:124432/1‑148 (MQ=255)
                                                                           tCCGTCAACGGCGGATTTAAAATGCCATGAGCCATTTACGCACGTTTGTTATTACCGGCGC‑GGCAATTGGTTTGGG‑CCGCGCCGTCGC‑GGAAAGTTTTGCAGCCCAGGCCGAGCACCTTTTGATCTTGCTTGATCGGGATCTGGCaa                                                                         <  6:424778/147‑1 (MQ=255)
                                                                           tCCGTCAACGGCGGATTGAAAATGCCATGAGCCAGTTACGCACGATTGTGATTACCGGCGC‑GGCCAATGGTATTGG‑CCGCGCCGTCGC‑GGAAAGTTTTGCAGCCCAGGGCGAGCACCTTTTGATCTTGCTTGATCGGGATCt                                                                              >  7:150753/1‑142 (MQ=255)
                                                                                        gATTGAAAATGCCATGAGCCAGTTACGCACGATTGTGATTACCGGCGC‑GGCCAATGGTATTGG‑CCGCGCCGTCGC‑GGAAAGTTTTGCAGCCCAGGCCGAGCACCTTTTTATCTTGCTTGATCGGGATCTGGCAACCGTGCAGgggtggg                                                          >  6:337066/1‑149 (MQ=255)
                                                                                         aTTGAAAATGCCATGAGCCAGTTACGCACGATTGTGATTACCGGCGC‑GGCCAATGGTATTGG‑CCGCGCCGTCGC‑GGAAAGTTTTTCAGCCCAGGCCGCGCACCATTTGATCTTGCTTGATAGGGATCTGGCAACCTTGCAGgggtgggt                                                         >  6:381221/1‑149 (MQ=255)
                                                                                                   ccATGAGCCAGTTACGCACGATTGTGATTACCGGCGC‑GGCCAATGGTATTGG‑CCGCGCCGTCGC‑GGAAAGTTTTTCAGCCCAGGCCGAGCACCTTTTTATATTTCTTGATGGGGATATGGCAACCTTGCAGGGGTGGGTCACCGAGGGc                                               >  4:279177/1‑149 (MQ=255)
                                                                                                      tGAGCCAGTTACGCACGATTGTGATTACCGGCGC‑GGCCAATGGTATTTG‑CCCCGCCGTCGC‑GGTAAGTTTTTCACCCCACGGCGGGCACCGTTTTATATTTCGTGGTGGGGATCTTGCAACCGTGCAGGGGTGGGTGACCGAGGGCGa                                             >  4:317980/1‑148 (MQ=255)
                                                                                                                    aCGATTGTGATTACCGGCGC‑GGCCAATGGTTTTTG‑CCGCGGCGGGGC‑GGTAAGTTTTGGAGCCCAGGGCGAGGACCTTTTGATGGTTGGTGATCGGGATATGGCCAACATGGCGGGGTGGGTCACCGGGGGCGAATTTTCCGCACGGAt                              >  4:90851/1‑149 (MQ=255)
                                                                                                                              tcccgggCGC‑‑GCCAATGGTTTGGGCCCCCCCCGTCGC‑GGAAAGTTTTGCAGCCCAGGCCGAGCACCTTTTGATCTTGCTTGATCGGGATCTGGCAACCTTGCAGGGGTGGGTCACCGAGGGCGAATTTGCCGCTCGTATCGAAACCCAt                    <  4:228880/144‑1 (MQ=255)
                                                                                                                                cccGGCGC‑GCCCAATGTTCTGGGCCCGCGCCGTCGC‑GGAAAGTTTTGCAGCCCAGGCCGAGCACCTTTTGATCTTGCTTGATCGGGATCTGGCAACCTTGCAGGGGTGGGTCACCGAGGGCGAATTTGCCGCTCGTATCGAAACCCATc                   <  3:164978/148‑1 (MQ=255)
                                                                                                                                  ccggcc‑gGGCAATTGTTTTGGCCCGCGCCGTCGC‑GGAAAGTTTTGCAGCCCAGGCCGAGCACCTTTTGATCTTGCTTGATCGGGATCTGGCAACCTTGCAGGGGTGGGTCACCGAGGGCGAATTTGCCGCTCGTATCGAAACCCATCaa                 <  1:311454/144‑1 (MQ=255)
                                                                                                                                  cGGCGC‑GGCCAATACCATTGG‑CCGCGCCGTCGC‑GGAAAGTTTTGCAGCCCAGGCCGAGCACCTTTTGATCTTGCTTGATCGGGATCTGGCAACCTTGCAGGGGTGGGTCACCGAGGGCGAATTTGCCGCTCGTATCGAAACCCATCAAg                >  7:321430/1‑149 (MQ=255)
                                                                                                                                           ccAATGGTATTGG‑CCGCGCCGTCGC‑GGAAAGTTTTGCAGCCCAGGCCGAGCACCTTTTGATCTTGCTTGATCGGGATCTGGCAACCTTGCAGGGGTGGGTCACCGAGGGCGAATTTGCCGCTCGTAt                              <  5:381928/127‑1 (MQ=255)
                                                                                                                                           ccAATGGTATTGG‑CCGCGCCGTCGC‑GGAAAGTTTTGCAGCCCAGGCCGAGCACCTTTTGATCTTGCTTGATCGGGATCTGGCAACCTTGCAGGGGTGGGTCACCGAGGGCGAATTTGCCGCTCGTAt                              >  6:381928/1‑127 (MQ=255)
                                                                                                                                            cAATGGTATTGG‑CCGCGCCGTCGC‑GGAAAGTTTTGCAGCCCAGGCCGAGCACCTTTTGATCTTGCTTGATCGGGATCTGGCAACCTTGCAGGGGTGGGTCACCGAGGGCGAATTTGCCGCTCGTATCGAAACCCATCAAGCGAACATCg       >  3:346614/1‑149 (MQ=255)
                                                                                                                                             aaTGGTATTGG‑CGGCGCCGTCGC‑GGAAAGTTTTGCAGCCCAGGCCGAGCACCTTTTGATCTTGCTTGATCGGGATCTGGCAACCTTGCAGGGGTGGGTCACCGAGGGCGAATTTGCCGCTCGTATCGAAACCCATCAAGCGAACATCGc      <  4:360254/149‑1 (MQ=255)
                                                                                                                                             aaTGGTATTGG‑CCGCGCCGTCGC‑GGAAAGTTTTGCAGCCCAGGCCGAGCACCTTTTGATCTTGCTTGATCGGGATCTGGCAACCTTGCAGGGGTGGGTCACCGAGGGCGAATTTGCCGCTTGTATCGAAACCCATCAAGCGAACATCGc      >  4:345346/1‑149 (MQ=255)
                                                                                                                                             aaTGGTATTGG‑CCGCGCCGTCGC‑GGAAAGTTTTGCAGCCCAGGCCGAGCACCTTTTGATCTTGCTTGATCGGGATCTGGCAACCTTGCAGGGGTGGGTCACCGAGGGCGAATTTGCCGCTCGTATCGAAACCCATCAAGCGAACATCGc      >  4:143792/1‑149 (MQ=255)
                                                                                                                                             aaTGGTATTGG‑CCGCGCCGTCGC‑GGAAAGTTTTGCAGCCCAGGCCGAGCACCTTTTGATCTTGCTTGATCGGGATCTGGCAACCTTGCAGGGGTGGGTCACCGAGGGCGAAGTTGCCGCTCGTATCGATCCCCATCAAGCGAACATCGc      >  2:431036/1‑149 (MQ=255)
                                                                                                                                              aTGGTTTTGGCCCGCGCCGTCGC‑GGAAAGTTTTGCAGCCCAGGCCGAGCACCTTTTGATCTTGCTTGATCGGGATCTGGCAACCTTGCAGGGGTGGGTCACCGAGGGCGAATTTGCCGCTCGTATCGAAACCCATCAAGCGAACATCGc      <  7:392850/149‑1 (MQ=255)
                                                                                                                                                 gTATTGG‑CCGCGCCGTCGC‑GGAAAGTTTTGCAGCCCAGGCCGAGCACCTTTTGATCTTGCTTGATCGGGATCTGGCAACCTTGCAGGGGTGGGTCACCGAGGGCGAATTTGCCGCTCGTATCGAAACCCATCAAGCGAACATCGCCGAt  >  8:291867/1‑149 (MQ=255)
                                                                                                                                                   |                                                                                                                                                    
GCCCGGCCTGAAGAAATTGCCGACGCGGTGCTGTATCTGGCCGAGCGCGGCCTGTACATCACGGGCGAAGTCCTGTCCGTCAACGGCGGATTGAAAATGCCATGAGCCAGTTACGCACGATTGTGATTACCGGCGC‑GGCCAATGGTATTGG‑CCGCGCCGTCGC‑GGAAAGTTTTGCAGCCCAGGCCGAGCACCTTTTGATCTTGCTTGATCGGGATCTGGCAACCTTGCAGGGGTGGGTCACCGAGGGCGAATTTGCCGCTCGTATCGAAACCCATCAAGCGAACATCGCCGAT  >  NC_002947_CJ‑RC/3171628‑3171920

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A