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 878,242 G→A 41.1% intergenic (‑128/‑42) ribA ← / → pgpB GTP cyclohydrolase II/phosphatidylglycerophosphate phosphatase B

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE878,2420GA41.1% 36.1 / 60.0 85intergenic (‑128/‑42)ribA/pgpBGTP cyclohydrolase II/phosphatidylglycerophosphate phosphatase B
Reads supporting (aligned to +/- strand):  ref base G (22/28);  new base A (20/15);  total (42/43)
Fisher's exact test for biased strand distribution p-value = 2.74e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.84e-01

CACCTAATCACGACGCGTCGATCGTTCACGGAATGGCACAAATCTGTCAATTTTTCCTGGAACTGGCGTTTTCAGTTATGATTGTGGGACTTATCAAAAAGGAGAGGCCATGCGTTCGATTGCCAGACGTACCGC  >  minE/878175‑878309
                                                                   |                                                                   
cACCTACTCACGACGCGTCGATCGTTCACGGAATGGCACAAATCTGTCAATTTTTCCTGGAACTGGCGt                                                                    >  1:2982773/1‑69 (MQ=255)
cACCTAATCACGACGCGTCGATCGTTCACGGAATGGCACAAATCTGTCAATTTTTCCTGGAACTGGCGt                                                                    >  1:1690865/1‑69 (MQ=255)
cACCTAATCACGACGCGTCGATCGTTCACGGAATGGCACAAATCTGTCAATTTTTCCTGGAACTGGCGt                                                                    >  1:1157312/1‑69 (MQ=255)
cACCTAATCACGACGCGTCGATCGTTCACGGAATGGCACAAATCTGTCAATTTTTCCTGGAACTGGCGt                                                                    >  1:1614842/1‑69 (MQ=255)
cACCTAATCACGACGCGTCGATCGTTCACGGAATGGCACAAATCTGTCAATTTTTCCTGGAACTGGCGt                                                                    >  1:374951/1‑69 (MQ=255)
cACCTAATCACGACGCGTCGATCGTTCACGGAATGGCACAAATCTGTCAATTTTTCCTGGAACTGGCGt                                                                    >  1:941145/1‑69 (MQ=255)
cACCTAATCACGACGCGTCGATCGTTCACGGAATGGCACAAATCTGTCAATTTTTCCTGGAACTGGCGt                                                                    >  1:2633078/1‑69 (MQ=255)
cACCTAATCACGACGCGTCGATCGTTCACGGAATGGCACAAATCTGTCAATTTTTCCTGGAACTGGCGt                                                                    >  1:3077810/1‑69 (MQ=255)
     aaTCACGACGCGTCGATCGTTCACGGAATGGCACAAATCTGTCAATTTTTCCTGGAACTGGCATTTTCa                                                               >  1:3116547/1‑69 (MQ=255)
     aaTCACGACGCGTCGATCGTTCACGGAATGGCACAAATCTGTCAATTTTTCCTGGAACTGGCATTTTCa                                                               >  1:3432107/1‑69 (MQ=255)
     aaTCACGACGCGTCGATCGTTCACGGAATGGCACAAATCTGTCAATTTTTCCTGGAACTGGCATTTTCa                                                               >  1:3374941/1‑69 (MQ=255)
     aaTCACGACGCGTCGATCGTTCACGGAATGGCACAAATCTGTCAATTTTTCCTGGAACTGGCATTTTCa                                                               >  1:2262561/1‑69 (MQ=255)
     aaTCACGACGCGTCGATCGTTCACGGAATGGCACAAATCTGTCAATTTTTCCTGGAACTGGCATTTTCa                                                               >  1:3171156/1‑69 (MQ=255)
     aaTCACGACGCGTCGATCGTTCACGGAATGGCACAAATCTGTCAATTTTTCCTGGAACTGGCATTTTCa                                                               >  1:3157682/1‑69 (MQ=255)
     aaTCACGACGCGTCGATCGTTCACGGAATGGCACAAATCTGTCAATTTTTCCTGGAACTGGCATTTTCa                                                               >  1:431062/1‑69 (MQ=255)
     aaTCACGACGCGTCGATCGTTCACGGAATGGCACAAATCTGTCAATTTTTCCTGGAACTGGCATTTTCa                                                               >  1:2543995/1‑69 (MQ=255)
     aaTCACGACGCGTCGATCGTTCACGGAATGGCACAAATCTGTCAATTTTTCCTGGAACTGGCATTTTCa                                                               >  1:2630004/1‑69 (MQ=255)
     aaTCACGACGCGTCGATCGTTCACGGAATGGCACAAATCTGTCAATTTTTCCTGGAACTGGCATTTTCa                                                               >  1:2615010/1‑69 (MQ=255)
     aaTCACGACGCGTCGATCGTTCACGGAATGGCACAAATCTGTCAATTTTTCCTGGAACTGGCATTTTCa                                                               >  1:716476/1‑69 (MQ=255)
     aaTCACGACGCGTCGATCGTTCACGGAATGGCACAAATCTGTCAATTTTTCCTGGAACTGGCATTTTCa                                                               >  1:1074082/1‑69 (MQ=255)
     aaTCACGACGCGTCGATCGTTCACGGAATGGCACAAATCTGTCAATTTTTCCTGGAACTGGCATTTTCa                                                               >  1:125829/1‑69 (MQ=255)
     aaTCACGACGCGTCGATCGTTCACGGAATGGCACAAATCTGTCAATTTTTCCTGGAACTGGCATTTTCa                                                               >  1:918921/1‑69 (MQ=255)
     aaTCACGACGCGTCGATCGTTCACGGAATGGCACAAATCTGTCAATTTTTCCTGGAACTGGCATTTTCa                                                               >  1:901540/1‑69 (MQ=255)
     aaTCACGACGCGTCGATCGTTCACGGAATGGCACAAATCTGTCAATTTTTCCTGGAACTGGCATTTTCa                                                               >  1:643252/1‑69 (MQ=255)
     aaTCACGACGCGTCGATCGTTCACGGAATGGCACAAATCTGTCAATTTTTCCTGGAACTGGCATTTTCa                                                               >  1:606359/1‑69 (MQ=255)
     aaTCACGACGCGTCGATCGTTCACGGAATGGCACAAATCTGTCAATTTTTCCTGGAACTGGCATTTTCa                                                               >  1:552110/1‑69 (MQ=255)
     aaTCACGACGCGTCGATCGTTCACGGAATGGCACAAATCTGTCAATTTTTCCTGGAACTGGCATTTTCa                                                               >  1:1540579/1‑69 (MQ=255)
     aaTCACGACGCGTCGATCGTTCACGGAATGGCACAAATCTGTCAATTTTTACTGGAACTGGCATTTTCa                                                               >  1:1326532/1‑69 (MQ=255)
        cACGACGCGTCGATCGTTCACGGAATGGCACAAATCTGTCAATTTTTCCTGGAACTGGCGTTTTCAGt                                                             <  1:3235791/68‑1 (MQ=255)
        cACGACGCGTCGATCGTTCACGGAATGGCACAAATCTGTCAATTTTTCCTGGAACTGGCAttt                                                                  <  1:985329/63‑1 (MQ=255)
        cACGACGCGTCGATCGTTCACGGAATGGCACAAATCTGTCAATTTTTCCTGGAACTGGCAttt                                                                  <  1:852558/63‑1 (MQ=255)
        cACGACGCGTCGATCGTTCACGGAATGGCACAAATCTGTCAATTTTTCCTGGAACTGGCAttt                                                                  <  1:3395152/63‑1 (MQ=255)
        cACGACGCGTCGATCGTTCACGGAATGGCACAAATCTGTCAATTTTTCCTGGAACTGGCAttt                                                                  <  1:2949553/63‑1 (MQ=255)
        cACGACGCGTCGATCGTTCACGGAATGGCACAAATCTGTCAATTTTTCCTGGAACTGGCAttt                                                                  <  1:373433/63‑1 (MQ=255)
        cACGACGCGTCGATCGTTCACGGAATGGCACAAATCTGTCAATTTTTCCTGGAACTGGCAttt                                                                  <  1:1002554/63‑1 (MQ=255)
        cACGACGCGTCGATCGTTCACGGAATGGCACAAATCTGTCAATTTTTCCTGGAACTGGCAttt                                                                  <  1:526589/63‑1 (MQ=255)
        cACGACGCGTCGATCGTTCACGGAATGGCACAAATCTGTCAATTTTTCCTGGAACTGGCAttt                                                                  <  1:2331613/63‑1 (MQ=255)
        cACGACGCGTCGATCGTTCACGGAATGGCACAAATCTGTCAATTTTTCCTGGAACTGGCAttt                                                                  <  1:1537840/63‑1 (MQ=255)
        cACGACGCGTCGATCGTTCACGGAATGGCACAAATCTGTCAATTTTTCCTGGAACTGGCAttt                                                                  <  1:1524691/63‑1 (MQ=255)
        cACGACGCGTCGATCGTTCACGGAATGGCACAAATCTGTCAATTTTTCCTGGAACTGGCAttt                                                                  <  1:1515829/63‑1 (MQ=255)
        cACGACGCGTCGATCGTTCACGGAATGGCACAAATCTGTCAATTTTTCCTGGAACTGGCAttt                                                                  <  1:2344577/63‑1 (MQ=255)
        cACGACGCGTCGATCGTTCACGGAATGGCACAAATCTGTCAATTTTTCCTGGAACTGGCAttt                                                                  <  1:1263212/63‑1 (MQ=255)
         acgacgCGTCGATCGTTCACGGAATGGCACAAATCTGTCAATTTTTCCTGGAACTGGCGTTTTCAGtt                                                            >  1:2819622/1‑68 (MQ=255)
         acgacgCGTCGATCGTTCACGGAATGGCACAAATCTGTCAATTTTTCCTGGAACTGGCGTTTTCAGtt                                                            >  1:1997716/1‑68 (MQ=255)
         acgacgCGTCGATCGTTCACGGAATGGCACAAATCTGTCAATTTTTCCTGGAACTGGCGTTTTCAGtt                                                            >  1:298235/1‑68 (MQ=255)
         acgacgCGTCGATCGTTCACGGAATGGCACAAATCTGTCAATTTTTCCTGGAACTGGCGTTTTCAGtt                                                            >  1:3261819/1‑68 (MQ=255)
         acgacgCGTCGATCGTTCACGGAATGGCACAAATCTGTCAATTTTTCCTGGAACTGGCGTTTTCAGtt                                                            >  1:221527/1‑68 (MQ=255)
         acgacgCGTCGATCGTTCACGGAATGGCACAAATCTGTCAATTTTTCCTGGAACTGGCGTTTTCAGt                                                             >  1:1554185/1‑67 (MQ=255)
         acgacgCGTCGATCGTTCACGGAATGGCACAAATCTGTCAATTTTTCCTGGAACTGGCAttt                                                                  <  1:751334/62‑1 (MQ=255)
                 tCGATCGTTCACGGAATGGCACAAATCTGTCAATTTTTCCTGGAACTGGCAttt                                                                  <  1:2773184/54‑1 (MQ=255)
                      cGTTCACGGAATGGCACAAATCTGTCAATTTTTCCTGGAACTGGCGTTTTCAGTTATGATTGTGGGACt                                              <  1:3355310/69‑1 (MQ=255)
                          cACGGAATGGCACAAATCTGTCAATTTTTCCTGGAACTGGCGTTTTCAGTTATGATTGTGGGACTTAt                                           >  1:1390819/1‑68 (MQ=255)
                            cGGAATGGCACAAATCTGTCAATTTTTCCTGGAACTGGCGTTTTCAGTTATGATTGTGGGACTTATCa                                         <  1:2365916/68‑1 (MQ=255)
                                aTGGCACAAATCTGTCAATTTTTCCTGGAACTGGCGTTTTCAGTTATGATTGTGGGAGTTATCa                                         <  1:6552/64‑1 (MQ=255)
                                aTGGCACAAATCTGTCAATTTTTCCTGGAACTGGCGTTTTCAGTTATGATTGTGGGACTTATCAAAAAg                                    <  1:657282/69‑1 (MQ=255)
                                aTGGCACAAATCTGTCAATTTTTCCTGGAACTGGCGTTTTCAGTTATGATTGTGGGACTTATCAAAAAg                                    <  1:2603015/69‑1 (MQ=255)
                                aTGGCACAAATCTGTCAATTTTTCCTGGAACTGGCGTTTTCAGTTATGATTGTGGGACTTATCAAAAAg                                    <  1:460326/69‑1 (MQ=255)
                                aTGGCACAAATCTGTCAATTTTTCCTGGAACTGGCGTTTTCAGTTATGATTGTGGGACTTATCAAAAAg                                    <  1:1238870/69‑1 (MQ=255)
                                aTGGCACAAATCTGTCAATTTTTCCTGGAACTGGCGTTTTCAGTTATGATTGTGGGACTTATCAAAAAg                                    <  1:1894799/69‑1 (MQ=255)
                                aTGGCACAAATCTGTCAATTTTTCCTGGAACTGGCGTTTTCAGTTATGATTGTGGGACTTATCAAAAAg                                    <  1:2655142/69‑1 (MQ=255)
                                aTGGCACAAATCTGTCAATTTTTCCTGGAACTGGCGTTTTCAGTTATGATTGTGGGACTTATCAAAAAg                                    <  1:1322501/69‑1 (MQ=255)
                                aTGGCACAAATCTGTCAATTTTTCCTGGAACTGGCGTTTTCAGTTATGATTGTGGGACTTATCAAAAAg                                    <  1:2675697/69‑1 (MQ=255)
                                aTGGCACAAATCTGTCAATTTTTCCTGGAACTGGCGTTTTCAGTTATGATTGTGGGACTTATCAAAAAg                                    <  1:2063964/69‑1 (MQ=255)
                                aTGGCACAAATCTGTCAATTTTTCCTGGAACTGGCGTTTTCAGTTATGATTGTGGGACTTATCAAAAAg                                    <  1:2470295/69‑1 (MQ=255)
                                aTGGCACAAATCTGTCAATTTTTCCTGGAACTGGCGTTTTCAGTTATGATTGTGGGACTTATCAAAAAg                                    <  1:2459815/69‑1 (MQ=255)
                                   gCACAAATCTGTCAATTTTTCCTGGAACTGGCGTTTTCAGTTATGATTGTGGGACTTATCAAAAAGgag                                 <  1:2031281/69‑1 (MQ=255)
                                   gCACAAATCTGTCAATTTTTCCTGGAACTGGCGTTTTCAGTTATGATTGTGGGACTTATCAAAAAGgag                                 >  1:2868623/1‑69 (MQ=255)
                                       aaaTCTGTCAATTTTTCCTTGAACTGGCGTTTTCAGTTATGATTGTGGGACTTATCAAAAAGGAGAGGc                             <  1:1408873/69‑1 (MQ=255)
                                       aaaTCTGTCAATTTTTCCTGGAACTGGCGTTTTCAGTTATGATTGTGGGACTTATCAAAAAGGAGAGGc                             <  1:2529396/69‑1 (MQ=255)
                                       aaaTCTGTCAATTTTTCCTGGAACTGGCGTTTTCAGTTATGATTGTGGGACTTATCAAAAAGGAGAGGc                             <  1:1740510/69‑1 (MQ=255)
                                       aaaTCTGTCAATTTTTCCTGGAACTGGCGTTTTCAGTTATGATTGTGGGACTTATCAAAAAGGAGAGGc                             <  1:3372443/69‑1 (MQ=255)
                                       aaaTCTGTCAATTTTTCCTGGAACTGGCGTTTTCAGTTATGATTGTGGGACTTATCAAAAAGGAGAGGc                             <  1:2449185/69‑1 (MQ=255)
                                        aaTCTGTCAATTTTTCCTGGAACTGGCGTTTTCAGTTATGATTGTGGGACTTATCAAAAAGGAGAGGc                             <  1:846936/68‑1 (MQ=255)
                                         aTCTGTCAATTTTTCCTGGAACTGGCGTTTTCAGTTATGATTGTGGGACTTATCAAAAAGGAGAGGCCa                           <  1:585998/69‑1 (MQ=255)
                                         aTCTGTCAATTTTTCCTGGAACTGGCGTTTTCAGTTATGATTGTGGGACTTATCAAAAAGGAGAGGCCa                           <  1:81765/69‑1 (MQ=255)
                                         aTCTGTCAATTTTTCCTGGAACTGGCGTTTTCAGTTATGATTGTGGGACTTATCAAAAAGGAGAGGCCa                           <  1:3366366/69‑1 (MQ=255)
                                                aaTTTTTCCTGGAACTGGCGTTTTCAGTTATGATTGTGGGACTTATCAAAAAGGAGAGGCCATGCGTTc                    <  1:3412607/69‑1 (MQ=255)
                                                  tttttCCTGGAACTGGCGTTTTCAGTTATGATTGTGGGACTTATCAAAAAGGAGAGGCCATGCGTTCg                   <  1:3406823/68‑1 (MQ=255)
                                                  tttttCCTGGAACTGGCGTTTTCAGTTATGATTGTGGGACTTATCAAAAAGGAGAGGCCATGCGTTCg                   <  1:2878045/68‑1 (MQ=255)
                                                                  cGTTTTCAGTTATGATTGTGGGACTTATCAAAAAGGAGAGGCCATGCGTTCGATTGcc             >  1:2790399/1‑58 (MQ=255)
                                                                  cGTTTTCAGTTATGATTGTGGGACTTATCAAAAAGGAGAGGCCATGCGTTCGATTGCCAGACGTACCGc  >  1:1936691/1‑69 (MQ=255)
                                                                  cGTTTTCAGTTATGATTGTGGGACTTATCAAAAAGGAGAGGCCATGCGTTCGATTGCCAGACGTACCGc  >  1:703748/1‑69 (MQ=255)
                                                                  cGTTTTCAGTTATGATTGTGGGACTTATCAAAAAGGAGAGGCCATGCGTTCGATTGCCAGACGTACCGc  >  1:14263/1‑69 (MQ=255)
                                                                  cGTTTTCAGTTATGATTGTGGGACTTATCAAAAAGGAGAGGCCATGCGTTCGATTGCCAGACGTACCGc  >  1:747265/1‑69 (MQ=255)
                                                                  cGTTTTCAGTTATGATTGTGGGACTTATCAAAAAGGAGAGGCCATGCGTTCGATTGCCAGACGTACCGc  >  1:2645214/1‑69 (MQ=255)
                                                                   |                                                                   
CACCTAATCACGACGCGTCGATCGTTCACGGAATGGCACAAATCTGTCAATTTTTCCTGGAACTGGCGTTTTCAGTTATGATTGTGGGACTTATCAAAAAGGAGAGGCCATGCGTTCGATTGCCAGACGTACCGC  >  minE/878175‑878309

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