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 2,482,042 C→T 31.5% S274S (TCG→TCA)  mdtL ← multidrug efflux system protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,482,0420CT31.5% 90.2 / 47.5 98S274S (TCG→TCA) mdtLmultidrug efflux system protein
Reads supporting (aligned to +/- strand):  ref base C (48/19);  new base T (12/19);  total (60/38)
Fisher's exact test for biased strand distribution p-value = 3.37e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.27e-01

AGAAACCGCATGGGAAGGTGAAACGGCAAGAGTGATCCCCGCCGCCAGGAATAACACCTGCGAGGTGATCATCAACGTACGTGGCTTAAAAATTCCCAGCGCAAATGGCGTGGAGAATGAAACGGTC  >  minE/2481982‑2482108
                                                            |                                                                  
agaAACCGCATGGGAAGGTGAAACGGCAAGAGTGATCCCCGCCGCCAGGAATAACACCTGCGAGGTGat                                                            >  1:9460/1‑69 (MQ=255)
agaAACCGCATGGGAAGGTGAAACGGCAAGAGTGATCCCCGCCGCCAGGAATAACACCTGCGAGGTGat                                                            >  1:2114005/1‑69 (MQ=255)
agaAACCGCATGGGAAGGTGAAACGGCAAGAGTGATCCCCGCCGCCAGGAATAACACCTGCGAGGTGat                                                            >  1:2999288/1‑69 (MQ=255)
agaAACCGCATGGGAAGGTGAAACGGCAAGAGTGATCCCCGCCGCCAGGAATAACACCTGCGAGGTGat                                                            >  1:394961/1‑69 (MQ=255)
agaAACCGCATGGGAAGGTGAAACGGCAAGAGTGATCCCCGCCGCCAGGAATAACACCTGCGAGGTGat                                                            >  1:1306544/1‑69 (MQ=255)
agaAACCGCATGGGAAGGTGAAACGGCAAGAGTGATCCCCGCCGCCAGGAATAACACCTGCGAGGTGat                                                            >  1:1278551/1‑69 (MQ=255)
agaAACCGCATGGGAAGGTGAAACGGCAAGAGTGATCCCCGCCGCCAGGAATAACACCTGCGAGGTGat                                                            >  1:731080/1‑69 (MQ=255)
agaAACCGCATGGGAAGGTGAAACGGCAAGAGTGATCCCCGCCGCCAGGAATAACACCTGCGAGGTGat                                                            >  1:859670/1‑69 (MQ=255)
agaAACCGCATGGGAAGGTGAAACGGCAAGAGTGATCCCCGCCGCCAGGAATAACACCTGCGAGGTGat                                                            >  1:1072154/1‑69 (MQ=255)
agaAACCGCATGGGAAGGTGAAACGGCAAGAGTGATCCCCGCCGCCAGGAATAACACCTGCGAGGTGa                                                             >  1:308374/1‑68 (MQ=255)
 gaAACCGCATGGGAAGGTGAAACGGCAAGAGTGATCCCCGCCGCCAGGAATAACACCTGCGAGGTGatc                                                           <  1:2614429/69‑1 (MQ=255)
 gaAACCGCATGGGAAGGTGAAACGGCAAGAGTGATCCCCGCCGCCAGGAATAACACCTGCGAGGTGatc                                                           <  1:3434273/69‑1 (MQ=255)
    aCCGCATGGGAAGGTGAAACGGCAAGAGTGATCCCCGCCGCCAGGAATAACACCTGCGAGGTGatcatc                                                        >  1:2496813/1‑69 (MQ=255)
    aCCGCATGGGAAGGTGAAACGGCAAGAGTGATCCCCGCCGCCAGGAATAACACCTGCGAGGTGatcatc                                                        >  1:564543/1‑69 (MQ=255)
    aCCGCATGGGAAGGTGAAACGGCAAGAGTGATCCCCGCCGCCAGGAATAACACCTGCGAGGTGatcatc                                                        >  1:48690/1‑69 (MQ=255)
    aCCGCATGGGAAGGTGAAACGGCAAGAGTGATCCCCGCCGCCAGGAATAACACCTGCGAGGTGatcatc                                                        >  1:381238/1‑69 (MQ=255)
        cATGGGAAGGTGAAACGGCAAGAGTGATCCCCGCCGCCAGGAATAACACCTGCGAGGTGATCATCAacg                                                    <  1:1401925/69‑1 (MQ=255)
        cATGGGAAGGTGAAACGGCAAGAGTGATCCCCGCCGCCAGGAATAACACCTGCGAGGTGATCATCAacg                                                    <  1:1882033/69‑1 (MQ=255)
        cATGGGAAGGTGAAACGGCAAGAGTGATCCCCGCCGCCAGGAATAACACCTGCGAGGTGATCATCAacg                                                    <  1:748532/69‑1 (MQ=255)
          tGGGAAGGTGAAACGGCAAGAGTGATCCCCGCCGCCAGGAATAACACCTGCGAGGTGATCATCAacgta                                                  <  1:1286640/69‑1 (MQ=255)
           gggAAGGTGAAACGGCAAGAGTGATCCCCGCCGCCAGGAATAACACCTGCGAGGTGATCATCAacgta                                                  <  1:1461019/68‑1 (MQ=255)
           gggAAGGTGAAACGGCAAGAGTGATCCCCGCCGCCAGGAATAACACCTGCGAGGTGATCATCAacgta                                                  <  1:1205902/68‑1 (MQ=255)
           gggAAGGTGAAACGGCAAGAGTGATCCCCGCCGCCAGGAATAACACCTGCGAGGTGATCATCAacgta                                                  <  1:722509/68‑1 (MQ=255)
            ggAAGGTGAAACGGCAAGAGTGATCCCCGCCGCCAGGAATAACACCTGCGAGGTGatca                                                          >  1:2425619/1‑59 (MQ=255)
            ggAAGGTGAAACGGCAAGAGTGATCCCCGCCGCCAGGAATAACACCTGCGAGGTGATCATCAacgtacg                                                >  1:110173/1‑69 (MQ=255)
            ggAAGGTGAAACGGCAAGAGTGATCCCCGCCGCCAGGAATAACACCTGCGAGGTGATCATCAacgtac                                                 >  1:3077292/1‑68 (MQ=255)
              aaGGTGAAACGGCAAGGGTGATCCCCGCCGCCAGGAATAACACCTGTGAGGTGATCATCAACGTACGTg                                              >  1:979822/1‑69 (MQ=255)
              aaGGTGAAACGGCAAGGGTGATCCCCGCCGCCAGGAATAACACCTGTGAGGTGATCATCAACGTACGTg                                              >  1:2458419/1‑69 (MQ=255)
              aaGGTGAAACGGCAAGGGTGATCCCCGCCGCCAGGAATAACACCTGTGAGGTGATCATCAACGTACGTg                                              >  1:2174230/1‑69 (MQ=255)
              aaGGTGAAACGGCAAGGGTGATCCCCGCCGCCAGGAATAACACCTGTGAGGTGATCATCAACGTACGTg                                              >  1:2687913/1‑69 (MQ=255)
              aaGGTGAAACGGCAAGGGTGATCCCCGCCGCCAGGAATAACACCTGTGAGGTGATCATCAACGTACGTg                                              >  1:2688990/1‑69 (MQ=255)
              aaGGTGAAACGGCAAGGGTGATCCCCGCCGCCAGGAATAACACCTGTGAGGTGATCATCAACGTACGTg                                              >  1:2833445/1‑69 (MQ=255)
              aaGGTGAAACGGCAAGGGTGATCCCCGCCGCCAGGAATAACACCTGTGAGGTGATCATCAACGTACGTg                                              >  1:2888367/1‑69 (MQ=255)
              aaGGTGAAACGGCAAGGGTGATCCCCGCCGCCAGGAATAACACCTGTGAGGTGATCATCAACGTACGTg                                              >  1:329237/1‑69 (MQ=255)
              aaGGTGAAACGGCAAGGGTGATCCCCGCCGCCAGGAATAACACCTGTGAGGTGATCATCAACGTACGTg                                              >  1:648878/1‑69 (MQ=255)
              aaGGTGAAACGGCAAGGGTGATCCCCGCCGCCAGGAATAACACCTGTGAGGTGATCATCAACGTACGTg                                              >  1:720824/1‑69 (MQ=255)
              aaGGTGAAACGGCAAGGGTGATCCCCGCCGCCAGGAATAACACCTGTGAGGTGATCATCAACGTACGTg                                              >  1:2076200/1‑69 (MQ=255)
              aaGGTGAAACGGAAAGGGTGATCCCCGCCGCCAGGAATAACACCTGTGAGGTGATCATCAACGTACGTg                                              >  1:2729063/1‑69 (MQ=255)
               aGGTGAAACGGCAAGGGTGATCCCCGCCTCCAGGAATAACACCTGTGAGGTGat                                                            <  1:1351615/54‑1 (MQ=255)
               aGGTGAAACGGCAAGGGTGATCCCCGCCGCCAGGAATAACACCTGTGAGGTGat                                                            <  1:1060977/54‑1 (MQ=255)
               aGGTGAAACGGCAAGGGTGATCCCCGCCGCCAGGAATAACACCTGTGAGGTGat                                                            <  1:2685738/54‑1 (MQ=255)
               aGGTGAAACGGCAAGGGTGATCCCCGCCGCCAGGAATAACACCTGTGAGGTGat                                                            <  1:2763644/54‑1 (MQ=255)
               aGGTGAAACGGCAAGGGTGATCCCCGCCGCCAGGAATAACACCTGTGAGGTGat                                                            <  1:2978668/54‑1 (MQ=255)
               aGGTGAAACGGCAAGGGTGATCCCCGCCGCCAGGAATAACACCTGTGAGGTGat                                                            <  1:1542561/54‑1 (MQ=255)
               aGGTGAAACGGCAAGGGTGATCCCCGCCGCCAGGAATAACACCTGTGAGGTGat                                                            <  1:3090771/54‑1 (MQ=255)
               aGGTGAAACGGCAAGGGTGATCCCCGCCGCCAGGAATAACACCTGTGAGGTGat                                                            <  1:1525164/54‑1 (MQ=255)
               aGGTGAAACGGCAAGGGTGATCCCCGCCGCCAGGAATAACACCTGTGAGGTGat                                                            <  1:1830842/54‑1 (MQ=255)
               aGGTGAAACGGCAAGGGTGATCCCCGCCGCCAGGAATAACACCTGTGAGGTGat                                                            <  1:3428771/54‑1 (MQ=255)
               aGGTGAAACGGCAAGGGTGATCCCCGCCGCCAGGAATAACACCTGTGAGGTGat                                                            <  1:1456763/54‑1 (MQ=255)
               aGGTGAAACGGCAAGGGTGATCCCCGCCGCCAGGAATAACACCTGTGAGGTGat                                                            <  1:203581/54‑1 (MQ=255)
               aGGTGAAACGGCAAGGGTGATCCCCGCCGCCAGGAATAACACCTGTGAGGTGat                                                            <  1:1328397/54‑1 (MQ=255)
               aGGTGAAACGGCAAGGGTGATCCCCGCCGCCAGGAATAACACCTGTGAGGTGat                                                            <  1:119141/54‑1 (MQ=255)
               aGGTGAAACGGCAAGGGTGATCCCCGCCGCCAGGAATAACACCTGTGAGGTGat                                                            <  1:1080847/54‑1 (MQ=255)
               aGGTGAAACGGCAAGGGTGATCCCCGCCGCCAGGAATAACACCTGTGAGGTGat                                                            <  1:782103/54‑1 (MQ=255)
               aGGTGAAACGGCAAGGGTGATCCCCGCCGCCAGGAATAACACCTGTGAGGTGat                                                            <  1:959204/54‑1 (MQ=255)
               aGGTGAAACGGCAAGGGTGATCCCCGCCACCAGGAATAACACCTGTGAGGTGat                                                            <  1:1035185/54‑1 (MQ=255)
               aGGGGAAACGGCAAGGCTGATCCCCGCCGCCAGGAATAACACCTGTGAGGGGat                                                            <  1:2684112/54‑1 (MQ=25)
                 gTGAAACGGCAAGAGTGATCCCCGCCGCCAGGAATAACACCTGCGAGGTGATCATCAACGTACGTGGc                                            >  1:1144929/1‑68 (MQ=255)
                 gTGAAACGGCAAGAGTGATCCCCGCCGCCAGGAATAACACCTGCGAGGTGATCATCAACGTACGTGGc                                            >  1:1778963/1‑68 (MQ=255)
                 gTGAAACGGCAAGAGTGATCCCCGCCGCCAGGAATAACACCTGCGAGGTGATCATCAACGTACGTGGc                                            >  1:1545318/1‑68 (MQ=255)
                      aCGGCAAGAGTGATCCCCGCCGCCAGGAATAACACCTGCGAGGTTATCATCAACGTACGTGGCTTaaa                                       <  1:3321248/68‑1 (MQ=255)
                      aCGGCAAGAGTGATCCCCGCCGCCAGGAATAACACCTGCGAGGTGATCATCAACGTACGTGGCTTaaa                                       <  1:3374453/68‑1 (MQ=255)
                      aCGGCAAGAGTGATCCCCGCCGCCAGGAATAACACCTGCGAGGTGATCATCAACGTACGTGGCTTaaa                                       <  1:1714474/68‑1 (MQ=255)
                      aCGGCAAGAGTGATCCCCGCCGCCAGGAATAACACCTGCGAGGTGATCATCAACGTACGTGGCTTaaa                                       <  1:3274504/68‑1 (MQ=255)
                      aCGGCAAGAGTGATCCCCGCCGCCAGGAATAACACCTGCGAGGTGATCATCAACGTACGTGGCTTaaa                                       <  1:412428/68‑1 (MQ=255)
                      aCGGCAAGAGTGATCCCCGCCGCCAGGAATAACACCTGCGAGGTGATCATCAACGTACGTGGCTTaaa                                       <  1:477424/68‑1 (MQ=255)
                      aCGGCAAGAGTGATCCCCGCCGCCAGGAATAACACCTGCGAGGTGATCATCAACGTACGTGGCTTaaa                                       <  1:1608461/68‑1 (MQ=255)
                      aCGGCAAGAGTGATCCCCGCCGCCAGGAATAACACCTGCGAGGTGATCATCAACGTACGTGGCTTaaa                                       <  1:12370/68‑1 (MQ=255)
                      aCGGCAAGAGTGATCCCCGCCGCCAGGAATAACACCTGCGAGGTGATCATCAACGTACGTGGCTTaaa                                       <  1:1200600/68‑1 (MQ=255)
                                tGATCCCCGCCGCCAGGAATAACACCTGCGAGGTGATCATCAACGTACGTGGCTTAAAAATTCCCAgc                             >  1:1071076/1‑68 (MQ=255)
                                tGATCCCCGCCGCCAGGAATAACACCTGCGAGGTGATCATCAACGTACGTGGCTTAAAAATTCCCAgc                             >  1:1735485/1‑68 (MQ=255)
                                  aTCCCCGCCGCCAGGAATAACACCTGCGAGGTGATCATCAacgt                                                   >  1:3337649/1‑44 (MQ=255)
                                  aTCCCCGCCGCCAGGAATAACACCTGCGAGGTGATCATCAACGTACGTGGCTTAAAAATTCCCAGCGCa                          >  1:2546910/1‑69 (MQ=255)
                                  aTCCCCGCCGCCAGGAATAACACCTGCGAGGTGATCATCAACGTACGTGGCTTAAAAATTCCCAGCGCa                          >  1:2391426/1‑69 (MQ=255)
                                  aTCCCCGCCGCCAGGAATAACACCTGCGAGGTGATCATCAACGTACGTGGCTTAAAAATTCCCAGCGCa                          >  1:2393539/1‑69 (MQ=255)
                                    ccccGCCGCCAGGAATAACACCTGCGAGGTGATCATCAACGTACGTGGCTTAAAAATTCCCAGCGCtaa                        >  1:2428436/1‑69 (MQ=255)
                                    ccccGCCGCCAGGAATAACACCTGCGAGGTGATCATCAACGTACGTGGCTTAAAAATTCCCAGCGCaaa                        >  1:1790330/1‑69 (MQ=255)
                                    ccccGCCGCCAGGAATAACACCTGCGAGGTGATCATCAACGTACGTGGCTTAAAAATTCCCAGCGCaaa                        >  1:444155/1‑69 (MQ=255)
                                           gccAGGAATAACACCTGCGAGGTGATCATCAACGTACGTGGCTTAAAAATTCCCAGCGCAAATGGCGTg                 <  1:2738953/69‑1 (MQ=255)
                                               ggAATAACACCTGCGAGGTGATCATCAACGTACGTGGCTTAAAAATTCCCAGCGCa                          >  1:2131690/1‑56 (MQ=255)
                                               ggAATAACACCTGCGAGGTGATCATCAACGTACGTGGCTTAAAAATTCCCAGCGCa                          >  1:618780/1‑56 (MQ=255)
                                                 aaTAACACCTGCGAGGTGATCATCAACGTACGTGGCTTAAAAATTCCCAGCGCAAATGGCGTGgag              >  1:2868210/1‑66 (MQ=255)
                                                 aaTAACACCTGCGAGGTGATCATCAACGTACGTGGCTTAAAAATTCCCAGCGCAAATGGCGTGgag              >  1:2358616/1‑66 (MQ=255)
                                                 aaTAACACCTGCGAGGTGATCATCAACGTACGTGGCTTAAAAATTCCCAGCGCAAATGGCGTGgag              >  1:1171552/1‑66 (MQ=255)
                                                 aaTAACACCTGCGAGGTGATCATCAACGTACGTGGCTTAAAAATTCCCAGCGCAAATGGCGTGgag              >  1:675208/1‑66 (MQ=255)
                                                 aaTAACACCTGCGAGGTGATCATCAACGTACGTGGCTTAAAAATTCCCAGCGCAAATGGCGTGgag              >  1:2448838/1‑66 (MQ=255)
                                                 aaTAACACCTGCGAGGTGATCATCAACGTACGTGGCTTAAAAATTCCCAGCGCAAATGGCGTGgag              >  1:1620714/1‑66 (MQ=255)
                                                 aaTAACACCTGCGAGGTGATCATCAACGTACGTGGCTTAAAAATTCCCAGCGCAAATGGCGTGgag              >  1:2662055/1‑66 (MQ=255)
                                                 aaTAACACCTGCGAGGTGATCATCAACGTACGTGGCTTAAAAATTCCCAGCGCAAATGGCGTGgag              >  1:3156716/1‑66 (MQ=255)
                                                 aaTAACACCTGCGAGGTGATCATCAACGTACGTGGCTTAAAAATTCCCAGCGCAAATGGCGTGgag              >  1:3213797/1‑66 (MQ=255)
                                                 aaTAACACCTGCGAGGTGATCATCAACGTACGTGGCTTAAAAATTCCCAGCGCAAATGGCGTGGAGaa            >  1:145455/1‑68 (MQ=255)
                                                     acacCTGCGAGGTGATCATCAACGTACGTGGCTTAAAAATTCCCAGCGCAAATGGCGTGGAGAATGaaa       >  1:2380329/1‑69 (MQ=255)
                                                     acacCTGCGAGGTGATCATCAACGTACGTGGCTTAAAAATTCCCAGCGCAAATGGCGTGGAGAATGaaa       >  1:462229/1‑69 (MQ=255)
                                                     acacCTGCGAGGTGATCATCAACGTACGTGGCTTAAAAATTCCCAGCGCAAATGGCGTGGAGAATGaaa       >  1:1714086/1‑69 (MQ=255)
                                                     acacCTGCGAGGTGATCATCAACGTACGTGGCTTAAAAATTCCCAGCGCAAATGGCGTGGAGAATGaaa       >  1:3172008/1‑69 (MQ=255)
                                                     acacCTGCGAGGTGATCATCAACGTACGTGGCTTAAAAATTCCCAGCGCAAATGGCGTGGAGAATGaaa       >  1:2050335/1‑69 (MQ=255)
                                                     acacCTGCGAGGTGATCATCAACGTACGTGGCTTAAAAATTCCCAGCGCAAATGGCGTGGAGAATGaaa       >  1:2131311/1‑69 (MQ=255)
                                                          tGCGAGGTGATCATCAACGTACGTGGCTTAAAAATTCCCAGCGCAAATGGCGTGGAGAATGAAACGGTc  >  1:2186128/1‑69 (MQ=255)
                                                            |                                                                  
AGAAACCGCATGGGAAGGTGAAACGGCAAGAGTGATCCCCGCCGCCAGGAATAACACCTGCGAGGTGATCATCAACGTACGTGGCTTAAAAATTCCCAGCGCAAATGGCGTGGAGAATGAAACGGTC  >  minE/2481982‑2482108

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A