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 2,337,184 A→G 39.6% S13S (TCA→TCG)  fdhE → formate dehydrogenase formation protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,337,1840AG39.6% 25.6 / 41.9 63S13S (TCA→TCG) fdhEformate dehydrogenase formation protein
Reads supporting (aligned to +/- strand):  ref base A (3/35);  new base G (15/10);  total (18/45)
Fisher's exact test for biased strand distribution p-value = 1.12e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCGCAAGACAACGGAAAAGAAAGCTGAATGAGTATTCGCATAATCCCGCAAGATGAGCTGGGTTCAAGCGAGAAACGTACGGCGGATATGATTCCGCCGTTATTGTTCCCTCGGCTCAAGAATTTATACA  >  minE/2337119‑2337248
                                                                 |                                                                
ccGCAAGACAACGGAAAAGAAAGCTGAATGAGTATTCGCATAATCCCGCAAGATGAGCTGGGTTCaa                                                                 >  1:2253635/1‑67 (MQ=255)
ccGCAAGACAACGGAAAAGAAAGCTGAATGAGTATTCGCATAATCCCGCAAGATGAGCTGGGTTCaa                                                                 >  1:950606/1‑67 (MQ=255)
ccGCAAGACAACGGAAAAGAAAGCTGAATGAGTATTCGCATAATCCCGCAAGATGAGCTGGGTTCaa                                                                 >  1:250543/1‑67 (MQ=255)
ccGCAAGACAACGGAAAAGAAAGCTGAATGAGTATTCGCATAATCCCGCAAGATGAGCTGGGTTCaa                                                                 >  1:2509444/1‑67 (MQ=255)
ccGCAAGACAACGGAAAAGAAAGCTGAATGAGTATTCGCATAATCCCGCAAGATGAGCTGGGTTCaa                                                                 >  1:2659579/1‑67 (MQ=255)
ccGCAAGACAACGGAAAAGAAAGCTGAATGAGTATTCGCATAATCCCGCAAGATGAGCTGGGTTCaa                                                                 >  1:1523696/1‑67 (MQ=255)
ccGCAAGACAACGGAAAAGAAAGCTGAATGAGTATTCGCATAATCCCGCAAGATGAGCTGGGATCa                                                                  >  1:1399603/1‑66 (MQ=255)
ccGCAAGACAACGGAAAAGAAAGCTGAATGAGTATTCGCATAAGCCCGCAAGATGAGCTGGGTTCaa                                                                 >  1:611044/1‑67 (MQ=255)
 cGCAAGACAACGGAAAAGAAAGCTGAATGAGTATTCGCATAATCCCGCAAGATGAGCTGGGTTCaa                                                                 >  1:2807687/1‑66 (MQ=255)
 cGCAAGACAACGGAAAAGAAAGCTGAATGAGTATTCGCATAATCCCGCAAGATGAGCTGGGTTCaa                                                                 >  1:895739/1‑66 (MQ=255)
 cGCAAGACAACGGAAAAGAAAGCTGAATGAGTATTCGCATAATCCCGCAAGATGAGCTGGGTTCaa                                                                 >  1:122461/1‑66 (MQ=255)
    aaGACAACGGAAAAGAAAGCTGAATGAGTATTCGCATAATCCCGCAAGATGAGCTGGGTTCAAGCgaga                                                           <  1:982069/69‑1 (MQ=255)
        cAACGGAAAAGAAAGCTGAATGAGTATTCGCATAATCCCGCAAGATGAGCTGGGTTCAAGCGAGAAACg                                                       <  1:1621057/69‑1 (MQ=255)
        cAACGGAAAAGAAAGCTGAATGAGTATTCGCATAATCCCGCAAGATGAGCTGGGTTCAAGCGAGAAACg                                                       <  1:2312962/69‑1 (MQ=255)
        cAACGGAAAAGAAAGCTGAATGAGTATTCGCATAATCCCGCAAGATGAGCTGGGTTCAAGCGAGAAACg                                                       <  1:231150/69‑1 (MQ=255)
                aagaaagCTGAATGAGTATTCGCATAATCCCGCAAGATGAGCTGGGTTCGAGCGAGAAACg                                                       >  1:2258824/1‑61 (MQ=255)
                aagaaagCTGAATGAGTATTCGCATAATCCCGCAAGATGAGCTGGGTTCGAGCGAGAAACGt                                                      >  1:2483281/1‑62 (MQ=255)
                aagaaagCTGAATGAGTATTCGCATAATCCCGCAAGATGAGCTGGGTTCGAGCGAGAAACGTAcggcg                                                >  1:291354/1‑68 (MQ=255)
                aagaaagCTGAATGAGTATTCGCATAATCCCGCAAGATGAGCTGGGTTCGAGCGAGAAACGTAcggcg                                                >  1:2872163/1‑68 (MQ=255)
                aagaaagCTGAATGAGTATTCGCATAATCCCGCAAGATGAGCTGGGTTCGAGCGAGAAACGTAcggcg                                                >  1:562239/1‑68 (MQ=255)
                aagaaagCTGAATGAGTATTCGCATAATCCCGCAAGATGAGCTGGGTTCGAGCGAGAAACGTAcggcg                                                >  1:252899/1‑68 (MQ=255)
                aagaaagCTGAATGAGTATTCGCATAATCCCGCAAGATGAGCTGGGTTCGAGCGAGAAACGTAcggcg                                                >  1:2756066/1‑68 (MQ=255)
                aagaaagCTGAATGAGTATTCGCATAATCCCGCAAGATGAGCTGGGTTCGAGCGAGAAACGTAcggcg                                                >  1:584641/1‑68 (MQ=255)
                aagaaagCTGAATGAGTATTCGCATAATCCCGCAAGATGAGCTGGGTTCGAGCGAGAAACGTAcggcg                                                >  1:256883/1‑68 (MQ=255)
                aagaaagCTGAATGAGTATTCGCATAATCCCGCAAGATGAGCTGGGTTCGAGCGAGAAACGTAcggcg                                                >  1:1411974/1‑68 (MQ=255)
                aagaaagCTGAATGAGTATTCGCATAATCCCGCAAGATGAGCTGGGTTCGAGCGAGAAACGTAcggcg                                                >  1:1188622/1‑68 (MQ=255)
                aagaaagCTGAATGAGTATTCGCATAATCCCGCAAGATGAGCTGGGTTCGAGCGAGAAACGTAcggcg                                                >  1:1426794/1‑68 (MQ=255)
                aagaaagCTGAATGAGTATTCGCATAATCCCGCAAGATGAGCTGGGTTCGAGCGAGAAACGTAcggcg                                                >  1:1676717/1‑68 (MQ=255)
                aagaaagCTGAATGAGTATTCGCATAATCCCGCAAGATGAGCTGGGTTCGAGCGAGAAACGTAcggcg                                                >  1:1704810/1‑68 (MQ=255)
                aagaaagCTGAATGAGTATTCGCATAATCCCGCAAGATGAGCTGGGTTCGAGCGAGAAACGTAcggcg                                                >  1:2123429/1‑68 (MQ=255)
                 agaaagCTGAATGAGTATTCGCATAATCCCGCAAGATGAGCTGGGTTCAAGCGAGAAACGTACGGCGGa                                              <  1:1321550/69‑1 (MQ=255)
                    aagGTGAATGAGTATTCGCATAATCCCGCAAGATGAGCTGGGTTCGAGCGAGAAACGTACGGCGGatat                                           <  1:959326/69‑1 (MQ=255)
                    aagCTGAATGAGTATTCGCATAATCCCGCAAGATGAGCTGGGTTCGAGCGAGAAACGTACGGCGGatat                                           <  1:2311777/69‑1 (MQ=255)
                    aagCTGAATGAGTATTCGCATAATCCCGCAAGATGAGCTGGGTTCGAGCGAGAAACGTACGGCGGatat                                           <  1:945022/69‑1 (MQ=255)
                    aagCTGAATGAGTATTCGCATAATCCCGCAAGATGAGCTGGGTTCGAGCGAGAAACGTACGGCGGatat                                           <  1:772534/69‑1 (MQ=255)
                    aagCTGAATGAGTATTCGCATAATCCCGCAAGATGAGCTGGGTTCGAGCGAGAAACGTACGGCGGatat                                           <  1:645805/69‑1 (MQ=255)
                    aagCTGAATGAGTATTCGCATAATCCCGCAAGATGAGCTGGGTTCGAGCGAGAAACGTACGGCGGatat                                           <  1:1300879/69‑1 (MQ=255)
                    aagCTGAATGAGTATTCGCATAATCCCGCAAGATGAGCTGGGTTCGAGCGAGAAACGTACGGCGGatat                                           <  1:3050821/69‑1 (MQ=255)
                    aagCTGAATGAGTATTCGCATAATCCCGCAAGATGAGCTGGGTTCGAGCGAGAAACGTACGGCGGatat                                           <  1:297638/69‑1 (MQ=255)
                    aagCTGAATGAGTATTCGCATAATCCCGCAAGATGAGCTGGGTTCGAGCGAGAAACGTACGGCGGatat                                           <  1:2835373/69‑1 (MQ=255)
                    aagCTGAATGAGTATTCGCATAATCCCGCAAGATGAGCTGGGTTCGAGCGAGAAACGTACGGCGGatat                                           <  1:1977492/69‑1 (MQ=255)
                    aagCTGAATGAGTATTCGCATAATCCCGCAAGATGAGCTGGGTTCAAGCGAGAAACGTACGGCGGatat                                           <  1:788115/69‑1 (MQ=255)
                    aagCTGAATGAGTATTCGCATAATCCCGCAAGATGAGCTGGGTTCAAGCGAGAAACGTACGGCGGatat                                           <  1:1894777/69‑1 (MQ=255)
                    aagCTGAATGAGTATTCGCATAATCCCGCAAGATGAGCTGGGTTCAAGCGAGAAACGTACGGCGGatat                                           <  1:1221983/69‑1 (MQ=255)
                    aagCTGAATGAGTATTCGCATAATCCCGCAAGATGAGCTGGGTTCAAGCGAGAAACGTACGGCGGatat                                           <  1:3324681/69‑1 (MQ=255)
                    aagCTGAATGAGTATTCGCATAATCCCGCAAGATGAGCTGGGTTCAAGCGAGAAACGTACGGCGGatat                                           <  1:304023/69‑1 (MQ=255)
                    aagCTGAATGAGTATTCGCATAATCCCGCAAGATGAGCTGGGTTCAAGCGAGAAACGTACGGCGGatat                                           <  1:2909895/69‑1 (MQ=255)
                    aagCTGAATGAGTATTCGCATAATCCCGCAAGATGAGCTGGGTTCAAGCGAGAAACGTACGGCGGatat                                           <  1:1730485/69‑1 (MQ=255)
                             gAGTATTCGCATAATCCCGCAAGATGAGCTGGGTTCAAGCGAGAAACGTACGGCGGATATGATTccgcc                                  <  1:3224747/69‑1 (MQ=255)
                             gAGTATTCGCATAATCCCGCAAGATGAGCTGGGTTCAAGCGAGAAACGTACGGCGGATATGATTccgcc                                  <  1:1234928/69‑1 (MQ=255)
                                tATTCGCATAATCCCGCAAGATGAGCTGGGTTCAAGCGAGAAACGTACGGCGGatat                                           <  1:2593016/57‑1 (MQ=255)
                                    cGCATAATCCCGCAAGATGAGCTTGGTTCAAGCGAGAAACGTACGGCGGatat                                           <  1:3120278/53‑1 (MQ=255)
                                    cGCATAATCCCGCAAGATGAGCTGGGTTCAAGCGAGAAACGTACGGCGGatat                                           <  1:44769/53‑1 (MQ=255)
                                    cGCATAATCCCGCAAGATGAGCTGGGTTCAAGCGAGAAACGTACGGCGGatat                                           <  1:2277537/53‑1 (MQ=255)
                                    cGCATAATCCCGCAAGATGAGCTGGGTTCAAGCGAGAAACGTACGGCGGatat                                           <  1:2474841/53‑1 (MQ=255)
                                    cGCATAATCCCGCAAGATGAGCTGGGTTCAAGCGAGAAACGTACGGCGGatat                                           <  1:695195/53‑1 (MQ=255)
                                    cGCATAATCCCGCAAGATGAGCTGGGTTCAAGCGAGAAACGTACGGCGGatat                                           <  1:1915197/53‑1 (MQ=255)
                                    cGCATAATCCCGCAAGATGAGCTGGGTTCAAGCGAGAAACGTACGGCGGatat                                           <  1:2790651/53‑1 (MQ=255)
                                    cGCATAATCCCGCAAGATGAGCTGGGTTCAAGCGAGAAACGTACGGCGGatat                                           <  1:1565057/53‑1 (MQ=255)
                                    cGCATAATCCCGCAAGATGAGCTGGGTTCAAGCGAGAAACGTACGGCGGatat                                           <  1:422528/53‑1 (MQ=255)
                                    cGCATAATCCCGCAAGATGAGCTGGGTTCAAGCGAGAAACGTACGGCGGatat                                           <  1:3419157/53‑1 (MQ=255)
                                    cGCATAATCCCGCAAGATGAGCTGGGTTCAAGCGAGAAACGTACGGCGGatat                                           <  1:2814043/53‑1 (MQ=255)
                                    cGCATAATCCCGCAAGATGAGCTGGGTTCAAGCGAGAAACGTACGGCGGatat                                           <  1:2092310/53‑1 (MQ=255)
                                         aaTCCCGCAAGATGAGCTGGGTTCAAGCGAGAAACGTACGGCGGATATGATTcc                                     >  1:2001025/1‑54 (MQ=255)
                                         aaTCCCGCAAGATGAGCTGGGTTCAAGCGAGAAACGTACGGCGGATATGATTCCGCCGTTATTGTTccc                      >  1:632346/1‑69 (MQ=255)
                                         aaTCCCGCAAGATGAGCTGGGTTCAAGCGAGAAACGTACGGCGGATATGATTCCGCCGTTATTGTTccc                      >  1:1123033/1‑69 (MQ=255)
                                          aTCCCGCAAGATGAGCTGGGTTCAAGCGAGAAACGTACGGCGGatat                                           <  1:2151234/47‑1 (MQ=255)
                                               gCAAGATGAGCTGGGTTCAAGCGAGAAACGTACGGCGGatat                                           <  1:1396149/42‑1 (MQ=255)
                                                      gAGCTGGGTTCAAGCGAGAACCGTACGGCGGatat                                           <  1:3195445/35‑1 (MQ=255)
                                                       aGCTGGGTTCAAGCGAGAAACGTACGGCGGATATGATTCCGCCGTTATTGTTCCCTCGGCTCAAGAAtt        <  1:2291806/69‑1 (MQ=255)
                                                       aGCTGGGTTCAAGCGAGAAACGTACGGCGGATATGATTCCGCCGTTATTGTTCCCTCGGCTCAAGAAtt        <  1:2579924/69‑1 (MQ=255)
                                                              ttCAAGCGAGAAACGTACGGCGGATATGATTCCGCCGTTATTGTTCCCTCGGCTCAAGAATTTATACa  <  1:1853015/68‑1 (MQ=255)
                                                              ttCAAGCGAGAAACGTACGGCGGATATGATTCCGCCGTTATTGTTCCCTCGGCTCAAGAATTTATACa  <  1:334970/68‑1 (MQ=255)
                                                               tCAAGCGAGAAACGTACGGCGGATATGATTCCGCCGTTATTGTTCCCTCGGCTCAAGAATTTATACa  <  1:2426766/67‑1 (MQ=255)
                                                                 |                                                                
CCGCAAGACAACGGAAAAGAAAGCTGAATGAGTATTCGCATAATCCCGCAAGATGAGCTGGGTTCAAGCGAGAAACGTACGGCGGATATGATTCCGCCGTTATTGTTCCCTCGGCTCAAGAATTTATACA  >  minE/2337119‑2337248

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

GATK/CNVnator alignment

N/A