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 1,469,159 C→T 34.9% V855I (GTT→ATT)  yfaL ← adhesin

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,469,1590CT34.9% 53.0 / 40.6 75V855I (GTT→ATT) yfaLadhesin
Reads supporting (aligned to +/- strand):  ref base C (36/12);  new base T (9/17);  total (45/30)
Fisher's exact test for biased strand distribution p-value = 1.08e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.85e-01

ATCAGCTGCGAAATCAACCACTTTAATGCCTGTCGATGTCGGCTCACCAATCCCTGTAATGGAGTTAACCACCACAGTTGTGTTGCCAGCAGTATTACCGTTCATCACCAATTGATCGCTTACCGAGTCATCG  >  minE/1469091‑1469223
                                                                    |                                                                
aTCAGCTGCGAAATCAACCACTTTAATGCCTGTCGATGTCGGCTCACCAATCCCTGTAATGGAGTTAac                                                                  <  1:1041341/69‑1 (MQ=255)
aTCAGCTGCGAAATCAACCACTTTAATGCCTGTCGATGTCGGCTCACCAATCCCTGTAATGGAGTTAac                                                                  <  1:636658/69‑1 (MQ=255)
aTCAGCTGCGAAATCAACCACTTTAATGCCTGTCGATGTCGGCTCACCAATCCCTGTAATGGAGTTAac                                                                  <  1:2866891/69‑1 (MQ=255)
       gCGAAATCAACTACTTTAATACCTGTAGATGTCGGCTCACCAATACCCGTAATGGGGTTAATtaccacg                                                           >  1:705875/1‑68 (MQ=255)
       gCGAAATCAACTACTTTAATACCTGTAGATGTCGGCTCACCAATACCCGTAATGGGGTTAATtaccacg                                                           >  1:618791/1‑68 (MQ=255)
       gCGAAATCAACTACTTTAATACCTGTAGATGTCGGCTCACCAATACCCGTAATGGGGTTAATtaccacg                                                           >  1:2515264/1‑68 (MQ=255)
       gCGAAATCAACTACTTTAATACCTGTAGATGTCGGCTCACCAATACCCGTAATGGGGTTAATtaccacg                                                           >  1:444036/1‑68 (MQ=255)
       gCGAAATCAACTACTTTAATACCTGTAGATGTCGGCTCACCAATACCCGTAATGGGGTTAATtaccacg                                                           >  1:1211409/1‑68 (MQ=255)
       gCGAAATCAACTACTTTAATACCTGTAGATGTCGGCTCACCAATACCCGTAATGGGGTTAATtaccacg                                                           >  1:1283206/1‑68 (MQ=255)
       gCGAAATCAACTACTTTAATACCTGTAGATGTCGGCTCACCAATACCCGTAATGGGGTTAATtaccacg                                                           >  1:2868881/1‑68 (MQ=255)
       gCGAAATCAACTACTTTAATACCTGTAGATGTCGGCTCACCAATACCCGTAATGGGGTTAATtaccacg                                                           >  1:1309246/1‑68 (MQ=255)
       gCGAAATCAACTACTTTAATACCTGTAGATGTCGGCTCACCAATACCCGTAATGGGGTTAATtaccacg                                                           >  1:301844/1‑68 (MQ=255)
          aaaTCAACCACTTTAATGCCTGTCGATGTCGGCTCACCAATCCCTGTAATGGAGTTAACCACCACAGt                                                         <  1:1833292/68‑1 (MQ=255)
          aaaTCAACCACTTTAATGCCTGTCGATGTCGGCTCACCAATCCCTGTAATGGAGTTAACCACCACAGt                                                         <  1:1905776/68‑1 (MQ=255)
          aaaTCAACCACTTTAATGCCTGTCGATGTCGGCTCACCAATCCCTGTAATGGAGTTAACCACCACAGt                                                         <  1:2675991/68‑1 (MQ=255)
          aaaTCAACCACTTTAATGCCTGTCGATGTCGGCTCACCAATCCCTGTAATGGAGTTAACCACCACAGt                                                         <  1:304852/68‑1 (MQ=255)
          aaaTCAACCACTTTAATGCCTGTCGATGTCGGCTCACCAATCCCTGTAATGGAGTTAACCACCACAGt                                                         <  1:490794/68‑1 (MQ=255)
          aaaTCAACCACTTTAATGCCTGTCGATGTCGGCTCACCAATCCCTGTAATGGAGTTAAACACCACAGt                                                         <  1:1322917/68‑1 (MQ=255)
                  cACTTTAATGCCTGTCGATGTCGGCTCA‑CAATCCCTGTAATGGAGTTAACCACCACAGTTGTGTTGcc                                                >  1:1264997/1‑68 (MQ=255)
                         aTGCCTGTCGATGTCGGCTCACCAATCCCTGTAATGGAGTTAACCACCACAGTTGTGTTGCcagcag                                           <  1:3428359/67‑1 (MQ=255)
                         aTGCCTGTCGATGTCGGCTCACCAATCCCTGTAATGGAGTTAACCACCACAGTTGTGTTGCcagcag                                           <  1:974050/67‑1 (MQ=255)
                         aTGCCTGTCGATGTCGGCTCACCAATCCCTGTAATGGAGTTAACCACCACAGTTGTGTTGCCAGCAGt                                          <  1:3279426/68‑1 (MQ=255)
                         aTGCCTGTCGATGTCGGCTCACCAATCCCTGTAATGGAGTTAACCACCACAGTTGTGTTGCCAGCAGt                                          <  1:1014206/68‑1 (MQ=255)
                         aTGCCTGTCGATGTCGGCTCACCAATCCCTGTAATGGAGTTAACCACCACAGTTGTGTTGCCAGCAGt                                          <  1:1443720/68‑1 (MQ=255)
                                           tCACCAATCCCTGTAATGGAGTTAACCACCACAGTTGTGTTGCCAGCAGTATTACCGTTCATCACCaa                        >  1:2511025/1‑68 (MQ=255)
                                           tCACCAATCCCTGTAATGGAGTTAACCACCACAGTTGTGTTGCCAGCAGTATTACCGTTCATCACCaa                        >  1:1856608/1‑68 (MQ=255)
                                           tCACCAATCCCTGTAATGGAGTTAACCACCACAGTTGTGTTGCCAGCAGTATTACCGTTCATCACCaa                        >  1:3348112/1‑68 (MQ=255)
                                           tCACCAATCCCTGTAATGGAGTTAACCACCACAGTTGTGTTGCCAGCAGTATTACCGTTCATCACCaa                        >  1:1192780/1‑68 (MQ=255)
                                           tCACCAATCCCTGTAATGGAGTTAACCACCACAGTTGTGTTGCCAGCAGTATTACCGTTCATCACCaa                        >  1:406401/1‑68 (MQ=255)
                                           tCACCAATCCCTGTAATGGAGTTAACCACCACAGTTGTGTTGCCAGCAGTATTACCGTTCATCACCaa                        >  1:393406/1‑68 (MQ=255)
                                           tCACCAATCCCTGTAATGGAGTTAACCACCACAGTTGTGTTGCCAGCAGTATTACCGTTCATCACCaa                        >  1:2099172/1‑68 (MQ=255)
                                           tCACCAATCCCTGTAATGGAGTTAACCACCACAGTTGTGTTCCCAGCAGTATTACCGTTCATCACCaa                        >  1:2105174/1‑68 (MQ=255)
                                              ccAATCCCTGTAATGGAGTTAACCACCACAGTTGTGTTGCcagcag                                           <  1:3432029/46‑1 (MQ=255)
                                                 aTCCCTGTAATGGAGTTAACCACCACAGTTGTGTTGCcagcat                                           <  1:704828/43‑2 (MQ=255)
                                                 aTCCCTGTAATGGAGTTAACCACCACAGTTGTGTTGCCAGCAGTATTACCGTTCATCACCAATTGATCg                 >  1:1392995/1‑69 (MQ=255)
                                                 aTCCCTGTAATGGAGTTAACCACCACAGTTGTGTTGCCAGCAGTATTACCGTTCATCACCAATTGATCg                 >  1:2865773/1‑69 (MQ=255)
                                                 aTCCCTGTAATGGAGTTAACCACCACAGTTGTGTTGCCAGCAGTATTACCGTTCATCACCAATTGATCg                 >  1:2639565/1‑69 (MQ=255)
                                                 aTCCCTGTAATGGAGTTAACCACCACAGTTGTGTTGCCAGCAGTATTACCGTTCATCACCAATTGATCg                 >  1:3283608/1‑69 (MQ=255)
                                                 aTCCCTGTAATGGAGTTAACCACCACAGTTGTGTTGCCAGCAGTATTACCGTTCATCACCAATTGATCg                 >  1:391902/1‑69 (MQ=255)
                                                 aTCCCTGTAATGGAGTTAACCACCACAGTTGTGTTGCCAGCAGTATTACCGTTCATCACCAATTGATCg                 >  1:589577/1‑69 (MQ=255)
                                                 aTCCCTGTAATGGAGTTAACCACCACAGTTGTGTTGCCAGCAGTATTACCGTTCATCACCAATTGATCg                 >  1:1807154/1‑69 (MQ=255)
                                                 aTCCCTGAAATGGAGTTAACCACCACAGTTGTGTTGCCAGCAGTATTACCGTTCATCACCAATTGATCg                 >  1:1081747/1‑69 (MQ=255)
                                                        tattGGGGTTAATTACCACGGCCGTGTTGCCAGCAGTATTACCGTTCAATACCAGTTGGTc                  <  1:245139/58‑1 (MQ=255)
                                                        tAATTGGGTTAATTACCACGGCCGTGTTGCCAGCAGTATTACCGTTCAATACCAGTTGGTc                  <  1:409562/61‑1 (MQ=255)
                                                        tAATGGGGTTAATTACCACGGCCGTGTTGCCATCAGTATTACCGTTCAATACCAGTTGGTc                  <  1:3432322/61‑1 (MQ=255)
                                                        tAATGGGGTTAATTACCACGGCCGTGTTGCCAGTAGTATTACCGTTCAATACCAGTTGGTc                  <  1:1644129/61‑1 (MQ=255)
                                                        tAATGGGGTTAATTACCACGGCCGTGTTGCCAGCAGTATTACCGTTCAATACCAGTTGGTc                  <  1:1147310/61‑1 (MQ=255)
                                                        tAATGGGGTTAATTACCACGGCCGTGTTGCCAGCAGTATTACCGTTCAATACCAGTTGGTc                  <  1:1138577/61‑1 (MQ=255)
                                                        tAATGGGGTTAATTACCACGGCCGTGTTGCCAGCAGTATTACCGTTCAATACCAGTTGGTc                  <  1:558650/61‑1 (MQ=255)
                                                        tAATGGGGTTAATTACCACGGCCGTGTTGCCAGCAGTATTACCGTTCAATACCAGTTGGTc                  <  1:3179100/61‑1 (MQ=255)
                                                        tAATGGGGTTAATTACCACGGCCGTGTTGCCAGCAGTATTACCGTTCAATACCAGTTGGTc                  <  1:1004468/61‑1 (MQ=255)
                                                        tAATGGGGTTAATTACCACGGCCGTGTTGCCAGCAGTATTACCGTTCAATACCAGTTGGTc                  <  1:2816263/61‑1 (MQ=255)
                                                        tAATGGGGTTAATTACCACGGCCGTGTTGCCAGCAGTATTACCGTTCAATACCAGTTGGTc                  <  1:1621669/61‑1 (MQ=255)
                                                        tAATGGGGTTAATTACCACGGCCGTGTTGCCAGCAGTATTACCGTTCAATACCAGTTGGTc                  <  1:1838768/61‑1 (MQ=255)
                                                        tAATGGGGTTAATTACCACGGCCGTGTTGCCAGCAGTATTACCGTTCAATACCAGTTGGTc                  <  1:1560909/61‑1 (MQ=255)
                                                        tAATGGGGTTAATTACCACGGCCGTGTTGCCAGCAGTATTACCGTTCAATACCAGTTGGTc                  <  1:19297/61‑1 (MQ=255)
                                                        tAATGGGGTTAATTACCACGGCCGTGTTGCCAGCAGTATTACCGTTCAATACCAGTTGGTc                  <  1:2264990/61‑1 (MQ=255)
                                                        tAATGGGGTAAATTACCACGGCCGTGTTGCCAGCAGTATTACCGTTCAATACCAGTTGGTc                  <  1:1090492/61‑1 (MQ=255)
                                                          aTGGAGTTAACCACCACAGTTGTGTTGCCAGCAGTATTACCGTTCATCACCAATTg                     >  1:2099020/1‑56 (MQ=255)
                                                          aTGGAGTTAACCACCACAGTTGTGTTGCCAGCAGTATTACCGTTCATCACCAATTg                     >  1:163178/1‑56 (MQ=255)
                                                          aTGGAGTTAACCACCACAGTTGTGTTGCCAGCAGTATTACCGTTCATCACCAATTg                     >  1:1796662/1‑56 (MQ=255)
                                                          aTGGAGTTAACCACCACAGTTGTGTTGCCAGCAGTATTACCGTTCATCACCAATTg                     >  1:2122644/1‑56 (MQ=255)
                                                          aTGGAGTTAACCACCACAGTTGTGTTGCCAGCAGTATTACCGTTCATCACCAATTg                     >  1:2173930/1‑56 (MQ=255)
                                                          aTGGAGTTAACCACCACAGTTGTGTTGCCAGCAGTATTACCGTTCATCACCAATTg                     >  1:1442680/1‑56 (MQ=255)
                                                           tGGGGTTAATTACCACGGCCGTGTTGCCAGCAGTATTACCGTTCAATACCAGTTGGTc                  <  1:1612916/58‑1 (MQ=255)
                                                             gAGTTAACCACCACAGTTGTGTTGCCAGCAGTATTACCGTTCATCACCAATTGATCGCTTACCGAGTc      >  1:1112648/1‑68 (MQ=255)
                                                             gAGTTAACCACCACAGTTGTGTTGCCAGCAGTATTACCGTTCATCACCAATTGATCGCTTACCGAGTCa     >  1:1425488/1‑69 (MQ=255)
                                                             gAGTTAACCACCACAGTTGTGTTGCCAGCAGTATTACCGTTCATCACCAATTGATCGCTTACCGAGTCa     >  1:203304/1‑69 (MQ=255)
                                                             gAGTTAACCACCACAGTTGTGTTGCCAGCAGTATTACCGTTCATCACCAATTGATCGCTTACCGAGTCa     >  1:1953842/1‑69 (MQ=255)
                                                             gAGTTAACCACCACAGTTGTGTTGCCAGCAGTATTACCGTTCATCACCAATTGATCGCTTACCGAGTCa     >  1:1931694/1‑69 (MQ=255)
                                                             gAGTTAACCACCACAGTTGTGTTGCCAGCAGTATTACCGTTCATCACCAATTGATCGCTTACCGAGTCa     >  1:2429039/1‑69 (MQ=255)
                                                             gAGTTAACCACCACAGTTGTGTTGCCAGCAGTATTACCGTTCATCACCAATTGATCGCTTACCGAGTCa     >  1:833991/1‑69 (MQ=255)
                                                             gAGTTAACCACCACAGTTGTGTTGCCAGCAGTATTACCGTTCATCACCAATTGATCGCTTACCGAGTCa     >  1:297439/1‑69 (MQ=255)
                                                               gTTAACCACCACAGTTGTGTTGCCAGCAGTATTACCGTTCATCACCAATTGATCGCTTACCGAGTCAt    >  1:3380542/1‑68 (MQ=255)
                                                               gTTAACCACCACAGTTGTGTTGCCAGCAGTATTACCGTTCATCACCAATTGATCGCTTACCGAGTCATc   >  1:1300895/1‑69 (MQ=255)
                                                               gTTAACCACCACAGTTGTGTTGCCAGCAGTATTACCGTTCATCACCAATTGATCGCTTACCGAGTCATc   >  1:3199933/1‑69 (MQ=255)
                                                               gTTAACCACCACAGTTGTGTTGCCAGCAGTATTACCGTTCATCACCAATTGATCGCTTAACGAGTCATc   >  1:180278/1‑69 (MQ=255)
                                                               gTTAACCACCACAGTTGTGTTGCCAGCAGTA‑TACCGTTCATCACCAATTGATCGCTTACCGAGTCATCg  >  1:1356022/1‑69 (MQ=255)
                                                                    |                                                                
ATCAGCTGCGAAATCAACCACTTTAATGCCTGTCGATGTCGGCTCACCAATCCCTGTAATGGAGTTAACCACCACAGTTGTGTTGCCAGCAGTATTACCGTTCATCACCAATTGATCGCTTACCGAGTCATCG  >  minE/1469091‑1469223

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