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 2,220,128 A→T 44.5% intergenic (+388/‑590) yhdH → / → accB predicted oxidoreductase, Zn‑dependent and NAD(P)‑binding/acetyl CoA carboxylase, BCCP subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,220,1280AT44.5% 29.6 / 98.4 92intergenic (+388/‑590)yhdH/accBpredicted oxidoreductase, Zn‑dependent and NAD(P)‑binding/acetyl CoA carboxylase, BCCP subunit
Reads supporting (aligned to +/- strand):  ref base A (28/23);  new base T (21/20);  total (49/43)
Fisher's exact test for biased strand distribution p-value = 8.34e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACTCGAACCTATTTAATGCTGAGCATTGTCAATCGGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCT  >  minE/2220062‑2220189
                                                                  |                                                             
aCTCGAACCTATTTAATGCTGAGCATTGTCAATCGGTTAATTTTGCGTGCTTTAGCATTCACATCTa                                                               >  1:1116774/1‑67 (MQ=255)
          aTTTAATGCTGAGGATTGTCAATCGGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGc                                                   <  1:641966/69‑1 (MQ=255)
          aTTTAATGCTGAGCATTGTCAATCGGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGc                                                   <  1:2660938/69‑1 (MQ=255)
          aTTTAATGCTGAGCATTGTCAATCGGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGc                                                   <  1:224186/69‑1 (MQ=255)
          aTTTAATGCTGAGCATTGTCAATCGGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGc                                                   <  1:1563751/69‑1 (MQ=255)
             tAATGCTGAGCATTGTCAATCGGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGCAg                                                 >  1:994167/1‑68 (MQ=255)
             tAATGCTGAGCATTGTCAATCGGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGCAg                                                 >  1:686730/1‑68 (MQ=255)
             tAATGCTGAGCATTGTCAATCGGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGCAg                                                 >  1:3190922/1‑68 (MQ=255)
             tAATGCTGAGCATTGTCAATCGGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGCAg                                                 >  1:1250360/1‑68 (MQ=255)
             tAATGCTGAGCATTGTCAATCGGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGCAg                                                 >  1:3008854/1‑68 (MQ=255)
             tAATGCTGAGCATTGTCAATCGGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGCAg                                                 >  1:107086/1‑68 (MQ=255)
             tAATGCTGAGCATTGTCAATCGGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGCAg                                                 >  1:1379174/1‑68 (MQ=255)
                  cTGAGCATTGTCAATCTGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGaa                                             <  1:2453476/67‑1 (MQ=255)
                  cTGAGCATTGTCAATCGGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGaaaa                                           >  1:2659609/1‑69 (MQ=255)
                  cTGAGCATTGTCAATCGGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGaaaa                                           >  1:2311658/1‑69 (MQ=255)
                  cTGAGCATTGTCAATCGGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATCCAGTGaa                                             <  1:2798390/67‑1 (MQ=255)
                       cATTGTCAATCGGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTgg                                       >  1:1949025/1‑68 (MQ=255)
                           gTCAATCGGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAAt                                  >  1:480035/1‑69 (MQ=255)
                           gTCAATCGGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAAt                                  >  1:1257900/1‑69 (MQ=255)
                           gTCAATCGGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAAt                                  >  1:2852399/1‑69 (MQ=255)
                           gTCAATCGGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAAt                                  >  1:3311580/1‑69 (MQ=255)
                           gTCAATCGGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAAt                                  >  1:3396810/1‑69 (MQ=255)
                           gTCAATCGGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAAt                                  >  1:3397861/1‑69 (MQ=255)
                           gTCAATCGGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAAt                                  >  1:3433526/1‑69 (MQ=255)
                           gTCAATCGGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAAt                                  >  1:398112/1‑69 (MQ=255)
                           gTCAATCGGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAAt                                  >  1:631302/1‑69 (MQ=255)
                           gTCAATCGGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAAt                                  >  1:728045/1‑69 (MQ=255)
                           gTCAATCGGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAAt                                  >  1:1329202/1‑69 (MQ=255)
                           gTCAATCGGTTAATTTTGAGTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAAt                                  >  1:1933953/1‑69 (MQ=255)
                              aaTCGGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCATACGATGCAGTGaa                                             <  1:2802793/55‑1 (MQ=255)
                              aaTCGGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGaa                                             <  1:966477/55‑1 (MQ=255)
                              aaTCGGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGaa                                             <  1:1118771/55‑1 (MQ=255)
                                  ggTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAATCCCCAGc                           >  1:1382272/1‑69 (MQ=255)
                                  ggTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAATCCCCAGc                           >  1:1823458/1‑69 (MQ=255)
                                  ggTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAATCCCCAGc                           >  1:1792074/1‑69 (MQ=255)
                                             cGTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGaa                                             <  1:2075797/40‑1 (MQ=255)
                                              gTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGt                <  1:3133097/68‑1 (MQ=255)
                                              gTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGt                <  1:810475/68‑1 (MQ=255)
                                              gTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGt                <  1:125766/68‑1 (MQ=255)
                                              gTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGt                <  1:3093408/68‑1 (MQ=255)
                                              gTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGt                <  1:672857/68‑1 (MQ=255)
                                              gTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGt                <  1:1178928/68‑1 (MQ=255)
                                              gTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGt                <  1:1083100/68‑1 (MQ=255)
                                              gTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGt                <  1:634487/68‑1 (MQ=255)
                                              gTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGt                <  1:1385690/68‑1 (MQ=255)
                                              gTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGt                <  1:2075920/68‑1 (MQ=255)
                                              gTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGt                <  1:2323723/68‑1 (MQ=255)
                                              gTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGt                <  1:1696831/68‑1 (MQ=255)
                                                   ttAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATgtc          <  1:1494461/69‑1 (MQ=255)
                                                       cATTCACATCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATgtcgtc       >  1:2450982/1‑68 (MQ=255)
                                                       cATTCACATCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATgtcgtc       >  1:338343/1‑68 (MQ=255)
                                                       cATTCACATCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATgtcgtc       >  1:2166093/1‑68 (MQ=255)
                                                       cATTCACATCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATgtcgtc       >  1:3087296/1‑68 (MQ=255)
                                                       cATTCACATCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATgtcgtc       >  1:3044518/1‑68 (MQ=255)
                                                       cATTCACATCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATgtcgtc       >  1:1978208/1‑68 (MQ=255)
                                                       cATTCACATCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATgtcgtc       >  1:524976/1‑68 (MQ=255)
                                                       cATTCACATCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATgtcgtc       >  1:567025/1‑68 (MQ=255)
                                                       cATTCACATCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATgtcgtc       >  1:1736179/1‑68 (MQ=255)
                                                       cATTCACATCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATgtcgtc       >  1:673946/1‑68 (MQ=255)
                                                       cATTCACATCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATgtcgtc       >  1:1666972/1‑68 (MQ=255)
                                                       cATTCACATCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATgtcgtc       >  1:1546423/1‑68 (MQ=255)
                                                       cATTCACATCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATgtcgtc       >  1:2713224/1‑68 (MQ=255)
                                                       cATTCACATCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATgtcgtc       >  1:2670217/1‑68 (MQ=255)
                                                       cATTCACATCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATgtcgtc       >  1:87845/1‑68 (MQ=255)
                                                       cATTCACATCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATgtcgt        >  1:2262544/1‑67 (MQ=255)
                                                       cATTCACATCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATgtcgt        >  1:2801618/1‑67 (MQ=255)
                                                       cATTCACATCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATgtcgt        >  1:2192144/1‑67 (MQ=255)
                                                       cATTCACATCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCt      >  1:3403391/1‑69 (MQ=255)
                                                       cATTCACATCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCt      >  1:3228466/1‑69 (MQ=255)
                                                       cATTCACATCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCt      >  1:2434730/1‑69 (MQ=255)
                                                           cacaTCTATCCAGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCt  >  1:24390/1‑69 (MQ=255)
                                                           cacaTCTATCCAGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCt  >  1:2006799/1‑69 (MQ=255)
                                                           cacaTCTATCCAGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCt  >  1:1319983/1‑69 (MQ=255)
                                                             caTCTTTCCGTACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCt  <  1:2814259/67‑1 (MQ=255)
                                                             caTCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCt  <  1:628599/67‑1 (MQ=255)
                                                             caTCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCt  <  1:1367205/67‑1 (MQ=255)
                                                             caTCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCt  <  1:1306017/67‑1 (MQ=255)
                                                             caTCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCt  <  1:2491338/67‑1 (MQ=255)
                                                             caTCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCt  <  1:2725639/67‑1 (MQ=255)
                                                             caTCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCt  <  1:2749602/67‑1 (MQ=255)
                                                             caTCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCt  <  1:2766524/67‑1 (MQ=255)
                                                             caTCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCt  <  1:2290816/67‑1 (MQ=255)
                                                             caTCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCt  <  1:1865242/67‑1 (MQ=255)
                                                             caTCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCt  <  1:194611/67‑1 (MQ=255)
                                                             caTCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCt  <  1:2151090/67‑1 (MQ=255)
                                                             caTCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCt  <  1:5957/67‑1 (MQ=255)
                                                             caTCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCt  <  1:286960/67‑1 (MQ=255)
                                                             caTCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCt  <  1:219241/67‑1 (MQ=255)
                                                             caTCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCt  <  1:199820/67‑1 (MQ=255)
                                                             caTCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCt  <  1:3166103/67‑1 (MQ=255)
                                                             caTCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCt  <  1:2037020/67‑1 (MQ=255)
                                                             caTCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCt  <  1:1243142/67‑1 (MQ=255)
                                                             caTCTTTCCGGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCt  <  1:3344092/67‑1 (MQ=255)
                                                                  |                                                             
ACTCGAACCTATTTAATGCTGAGCATTGTCAATCGGTTAATTTTGCGTGCTTTAGCATTCACATCTATCCAGACGATGCAGTGAAAATTGGGTAATCCCCAGCAACCGCTGCGTAATGTCGTCTATCT  >  minE/2220062‑2220189

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