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 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 889,789 C→T 49.4% A69T (GCC→ACC)  fabI ← enoyl‑[acyl‑carrier‑protein] reductase, NADH‑dependent

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE889,7890CT49.4% 1.5 / 81.3 90A69T (GCC→ACC) fabIenoyl‑[acyl‑carrier‑protein] reductase, NADH‑dependent
Reads supporting (aligned to +/- strand):  ref base C (24/21);  new base T (36/8);  total (60/30)
Fisher's exact test for biased strand distribution p-value = 6.28e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.73e-01

AGAGTGTACGAAACCGTCAAATTTCGGCCAAACTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGCATCTTCTGCAACATCGCACTGCAGAACGATGTCAGAACCCAATTGAGCGGCAAATTCTTC  >  minE/889721‑889849
                                                                    |                                                            
agagTGTACGAAACCGTCAAATTTCGGCCAAACTTTCCCCTGTTCAGCGAACATGGTGTCGATGCTGGc                                                              <  1:2656348/69‑1 (MQ=255)
agagTGTACGAAACCGTCAAATTTCGGCCAAACTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGc                                                              <  1:724843/69‑1 (MQ=255)
agagTGTACGAAACCGTCAAATTTCGGCCAAACTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGc                                                              <  1:54315/69‑1 (MQ=255)
agagTGTACGAAACCGTCAAATTTCGGCCAAACTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGc                                                              <  1:1425368/69‑1 (MQ=255)
 gagTGTACGAAACCGTCAAATTTCGGCCAAACTTTCCCCAGTTCAGCGATCATGGTGTCGATGCTGGCa                                                             <  1:2047050/69‑1 (MQ=255)
 gagTGTACGAAACCGTCAAATTTCGGCCAAACTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGCa                                                             <  1:1036114/69‑1 (MQ=255)
 gagTGTACGAAACCGTCAAATTTCGGCCAAACTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGCa                                                             <  1:972896/69‑1 (MQ=255)
 gagTGTACGAAACCGTCAAATTTCGGCCAAACTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGCa                                                             <  1:944910/69‑1 (MQ=255)
 gagTGTACGAAACCGTCAAATTTCGGCCAAACTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGCa                                                             >  1:3364267/1‑69 (MQ=255)
 gagTGTACGAAACCGTCAAATTTCGGCCAAACTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGCa                                                             <  1:3156546/69‑1 (MQ=255)
 gagTGTACGAAACCGTCAAATTTCGGCCAAACTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGCa                                                             <  1:2578801/69‑1 (MQ=255)
 gagTGTACGAAACCGTCAAATTTCGGCCAAACTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGCa                                                             <  1:2123315/69‑1 (MQ=255)
 gagTGTACGAAACCGTCAAATTTCGGCCAAACTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGCa                                                             <  1:1912091/69‑1 (MQ=255)
 gagTGTACGAAACCGTCAAATTTCGGCCAAACTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGCa                                                             <  1:1202392/69‑1 (MQ=255)
 gagTGTACGAAACCGTCAAAATTCGGCCAAACTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGCa                                                             <  1:3336523/69‑1 (MQ=255)
  agTGTACGAAACCGTCAAATTTCGGCCAAACTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGCa                                                             <  1:1130270/68‑1 (MQ=255)
      tACGAAACCGTCAAATTTCGTCCAAACTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGCAtcttc                                                        >  1:822556/1‑69 (MQ=255)
      tACGAAACCGTCAAATTTCGGCCAAACTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGCAtcttc                                                        >  1:3344624/1‑69 (MQ=255)
      tACGAAACCGTCAAATTTCGGCCAAACTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGCAtcttc                                                        >  1:3237611/1‑69 (MQ=255)
      tACGAAACCGTCAAATTTCGGCCAAACTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGCAtctt                                                         >  1:530355/1‑68 (MQ=255)
        cGAAACCGTCAAATTTCGGCCAAACTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGTAtcttcg                                                       >  1:699790/1‑67 (MQ=255)
        cGAAACCGTCAAATTTCGGCCAAACTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGTAtcttcg                                                       >  1:3379284/1‑67 (MQ=255)
        cGAAACCGTCAAATTTCGGCCAAACTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGTAtcttcg                                                       >  1:2882083/1‑67 (MQ=255)
        cGAAACCGTCAAATTTCGGCCAAACTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGTAtcttcg                                                       >  1:2624235/1‑67 (MQ=255)
        cGAAACCGTCAAATTTCGGCCAAACTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGTAtcttcg                                                       >  1:737793/1‑67 (MQ=255)
        cGAAACCGTCAAATTTCGGCCAAACTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGTAtcttcg                                                       >  1:2327337/1‑67 (MQ=255)
        cGAAACCGTCAAATTTCGGCCAAACTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGTAtcttcg                                                       >  1:13093/1‑67 (MQ=255)
        cGAAACCGTCAAATTTCGGCCAAACTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGTAtcttcg                                                       >  1:1115135/1‑67 (MQ=255)
        cGAAACCGTCAAATTTCGGCCAAACTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGTAtcttcg                                                       >  1:1510830/1‑67 (MQ=255)
           aaCCGTCAAATTTCGGCCAAACTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGCATCTTCTGCaa                                                   <  1:869366/69‑1 (MQ=255)
            aCCGTCAAATTTCGGCCAAACTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGCATCTTCTGCAAc                                                  <  1:464317/69‑1 (MQ=255)
            aCCGTCAAATTTCGGCCAAACTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGCATCTTCTGCAAc                                                  <  1:2917772/69‑1 (MQ=255)
                  aaaTTTCGGCCAAACTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGCATCTTCTGCAACATCGCa                                            <  1:2110659/69‑1 (MQ=255)
                  aaaTTTCGGCCAAACTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGCATCTTCTGCAACATCGCa                                            <  1:1006793/69‑1 (MQ=255)
                  aaaTTTCGGCCAAACTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGCATCTTCTGCAACATCGCa                                            <  1:2016248/69‑1 (MQ=255)
                  aaaTTTCGGCCAAACTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGCATCTTCTGCAACATCGCa                                            <  1:352618/69‑1 (MQ=255)
                  aaaTTTCGGCCAAACTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGCATCTTCTGCAACATCGCa                                            <  1:116362/69‑1 (MQ=255)
                  aaaTTTCGGCCAAACTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGCATCTTCTGCAACATCGCa                                            <  1:1896667/69‑1 (MQ=255)
                      ttCGGCCAAACTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGCa                                                             <  1:2934252/48‑1 (MQ=255)
                           ccAAACTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGc                                                              <  1:850779/42‑1 (MQ=255)
                             aaaCTTTCCCCAGTTCATCGAACATGGTGTCGATGCTGGTATCTTCGGCAACATCGCACTGCAGAACGa                                 >  1:3130281/1‑69 (MQ=255)
                             aaaCTTTCCCCAGTTCAGCGATCATGGTGTCGATGCTGGTATCTTCGGCAACATCGCACTGCAGAACGa                                 >  1:1522266/1‑69 (MQ=255)
                             aaaCTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGTAtc                                                           >  1:1680419/1‑43 (MQ=255)
                             aaaCTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGTAtc                                                           >  1:3237105/1‑43 (MQ=255)
                             aaaCTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGTATCTTCGGCAACAt                                                >  1:1242833/1‑54 (MQ=255)
                             aaaCTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGTATCTTCGGCAACATCGCACt                                          >  1:276150/1‑60 (MQ=255)
                             aaaCTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGTATCTTCGGCAACATCGCACTTCAGAACGa                                 >  1:2563975/1‑69 (MQ=255)
                             aaaCTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGTATCTTCGGCAACATCGCACTGCAGAACGa                                 <  1:1687085/69‑1 (MQ=255)
                             aaaCTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGTATCTTCGGCAACATCGCACTGCAGAACGa                                 >  1:1708393/1‑69 (MQ=255)
                             aaaCTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGTATCTTCGGCAACATCGCACTGCAGAACGa                                 >  1:3050890/1‑69 (MQ=255)
                             aaaCTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGTATCTTCGGCAACATCGCACTGCAGAACGa                                 >  1:1995353/1‑69 (MQ=255)
                             aaaCTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGTATCTTCGGCAACATCGCACTGCAGAACGa                                 >  1:831865/1‑69 (MQ=255)
                             aaaCTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGTATCTTCGGCAACATCGCACTGCAGAACGa                                 <  1:1236764/69‑1 (MQ=255)
                             aaaCTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGTATCTTCGGCAACATCGCACTGCAGAACGa                                 >  1:867180/1‑69 (MQ=255)
                             aaaCTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGTATCTTCGGCAACATCGCACTGCAGAACGa                                 >  1:2953023/1‑69 (MQ=255)
                             aaaCTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGTATCTTCGGCAACATCGCACTGCAGAACGa                                 >  1:3256744/1‑69 (MQ=255)
                             aaaCTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGTATCTTCGGCAACATCGCACTGCAGAACGa                                 <  1:3330384/69‑1 (MQ=255)
                             aaaCTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGTATCTTCGGCAACATCGCACTGCAGAACGa                                 >  1:164207/1‑69 (MQ=255)
                             aaaCTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGTATCTTCGGCAACATCGCACTGCAGAACGa                                 <  1:3353945/69‑1 (MQ=255)
                             aaaCTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGTATCTTCGGCAACATCGCACTGCAGAACGa                                 >  1:2110739/1‑69 (MQ=255)
                             aaaCTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGTATCTTCGGCAACATCGCACTGCAGAACGa                                 <  1:2363410/69‑1 (MQ=255)
                             aaaCTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGTATCTTCGGCAACATCGCACTGCAGAACGa                                 >  1:2410700/1‑69 (MQ=255)
                             aaaCTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGTATCTTCGGCAACATCGCACTGCAGAACGa                                 <  1:242215/69‑1 (MQ=255)
                             aaaCTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGTATCTTCGGCAACATCGCACTGCAGAACGa                                 >  1:561661/1‑69 (MQ=255)
                             aaaCTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGTATCTTCGGCAACATCGCACTGCAGAACGa                                 <  1:1785693/69‑1 (MQ=255)
                             aaaCTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGTATCTTCGGCAACATCGCACTGCAGAACGa                                 >  1:595883/1‑69 (MQ=255)
                             aaaCTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGTATCTTCGGCAACATCGCACTGCAGAACGa                                 >  1:2850506/1‑69 (MQ=255)
                             aaaCTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGTATCTTCGGCAACATCGCACTGCAGAACGa                                 >  1:2831509/1‑69 (MQ=255)
                             aaaCTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGTATCTTCGGCAACATCGCACTGCAGAACGa                                 >  1:2807076/1‑69 (MQ=255)
                             aaaCTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGTATCTTCGGCAACATCGCACTGCAGAACGa                                 <  1:2671601/69‑1 (MQ=255)
                             aaaCTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGTATCTTCGGCAACATCGCACTGCAGAACGa                                 >  1:2636983/1‑69 (MQ=255)
                             aaaCTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGTATCTTCGGCAACATCGCACTGCAGAACGa                                 >  1:1871937/1‑69 (MQ=255)
                             aaaCTTTCCCCAGTTCAGCGAACATGGTGTCGATGCAGGTATCTTCGGCAACATCGCACTGCAGAACGa                                 >  1:1614268/1‑69 (MQ=255)
                             aaaCTTT‑CCCAGTTCAGCGAACATGGTGTCGATGCTGGTATCTTCGGCAACATCGCACTGCAGAACGAt                                >  1:1995042/1‑69 (MQ=255)
                             aaaCTTACCCCAGTTCAGCGAACATGGTGTCGATGCTGGTATCTTCGGCAACATCGCACTGCAGAACGa                                 >  1:4953/1‑69 (MQ=255)
                                cTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGCATCTTCTGCAACATCGCACTGCAGAACGAt                                >  1:1597131/1‑67 (MQ=255)
                                cTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGCATCTTCTGCAACATCGCACTGCAGAACGAt                                >  1:2073323/1‑67 (MQ=255)
                                cTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGCATCTTCTGCAACATCGCACTGCAGAACGAt                                >  1:3108377/1‑67 (MQ=255)
                                cTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGCATCTTCTGCAACATCGCACTGCAGAACGAt                                >  1:2251660/1‑67 (MQ=255)
                                cTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGCATCTTCTGCAACATCGCACTGCAGAACGAt                                >  1:2936172/1‑67 (MQ=255)
                                cTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGCATCTTCTGCAACATCGCACTGCAGAACGAt                                >  1:2261933/1‑67 (MQ=255)
                                cTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGCATCTTCTGCAACATCGCACTGCAGAACGAt                                >  1:2874749/1‑67 (MQ=255)
                                cTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGCATCTTCTGCAACATCGCACTGCAGAACGAt                                >  1:2325537/1‑67 (MQ=255)
                                cTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGCATCTTCTGCAACATCGCACTGCAGAACGAt                                >  1:12453/1‑67 (MQ=255)
                                cTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGCATCTTCTGCAACATCGCACTGCAGAACGAt                                >  1:2501789/1‑67 (MQ=255)
                                           tCAGCGAACATGGTGTCGATGCTGGCATCTTCTGCAACAt                                                >  1:3023272/1‑40 (MQ=255)
                                           tCAGCGAACATGGTGTCGATGCTGGCATCTTCTGCAACATCGCACTGCATAACGATGTCAGAACCCaa                    >  1:997852/1‑68 (MQ=255)
                                           tCAGCGAACATGGTGTCGATGCTGGCATCTTCTGCAACATCGCACTGCAGAACGATGTCAGAACCCaa                    >  1:1466271/1‑68 (MQ=255)
                                            cAGCGAACATGGTTTCGATGCTGTGATCTTCTGCAACATGGCa                                            <  1:2899841/43‑1 (MQ=25)
                                                            gATGCTGGCATCTTCTGCAACATCGCACTGCAGAACGATGTCAGAACCCAATTGAGCGGCAAAttcttc  >  1:2474899/1‑69 (MQ=255)
                                                            gATGCTGGCATCTTCTGCAACATCGCACTGCAGAACGATGTCAGAACCCAATTGAGCGGCAAAttcttc  >  1:2601049/1‑69 (MQ=255)
                                                            gATGCTGGCATCTTCTGCAACATCGCACTGCAGAACGATGTCAGAACCCAATTGAGCGGCAAAttcttc  >  1:296156/1‑69 (MQ=255)
                                                            gATGCTGGCATCTTCTGCAACATCGCACTGCAGAACGATGTCAGAACCCAATTGAGCGGCAAAttcttc  >  1:2078304/1‑69 (MQ=255)
                                                            gATGCTGGCATCTTCTGCAACATCGCACTGCAGAACGATGTCAGAACCCAATTGAGCGGCAAAttcttc  >  1:3226571/1‑69 (MQ=255)
                                                            gATGCTGGCATCTTCTGCAACATCGCACTGCAGAACGATGTCAGAACCCAATTGAGCGGCAAAttcttc  >  1:3435165/1‑69 (MQ=255)
                                                                    |                                                            
AGAGTGTACGAAACCGTCAAATTTCGGCCAAACTTTCCCCAGTTCAGCGAACATGGTGTCGATGCTGGCATCTTCTGCAACATCGCACTGCAGAACGATGTCAGAACCCAATTGAGCGGCAAATTCTTC  >  minE/889721‑889849

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A