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 2,209,600 A→G 34.7% S647S (TCT→TCC)  yhdP ← conserved membrane protein, predicted transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,209,6000AG34.7% 63.4 / 53.0 92S647S (TCT→TCC) yhdPconserved membrane protein, predicted transporter
Reads supporting (aligned to +/- strand):  ref base A (49/11);  new base G (15/17);  total (64/28)
Fisher's exact test for biased strand distribution p-value = 8.48e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.37e-01

AAGATGTAAGCGAGCATTCACATCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGAGAATCTTTCAGCGGTGTCTCATCAAAGTAAGGGCCAACGGCTTTA‑CCCGGACCTTTA  >  minE/2209540‑2209657
                                                            |                                                          
aaGATGTAAGCGAGCATTCACATCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGAGAATCt                                                      >  1:995020/1‑67 (MQ=255)
aaGATGTAAGCGAGCATTCACATCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGAGAATCt                                                      >  1:965260/1‑67 (MQ=255)
aaGATGTAAGCGAGCATTCACATCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGAGAATCt                                                      >  1:2263684/1‑67 (MQ=255)
aaGATGTAAGCGAGCATTCACATCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGAGAATCt                                                      >  1:2908453/1‑67 (MQ=255)
aaGATGTAAGCGAGCATTCACATCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGAGAATCt                                                      >  1:844897/1‑67 (MQ=255)
aaGATGTAAGCGAGCATTCACATCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGAGAATCt                                                      >  1:2940310/1‑67 (MQ=255)
aaGATGTAAGCGAGCATTCACATCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGAGAATCt                                                      >  1:736701/1‑67 (MQ=255)
aaGATGTAAGCGAGCATTCACATCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGAGAATCt                                                      >  1:3375747/1‑67 (MQ=255)
aaGATGTAAGCGAGCATTCACATCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGAGAATCt                                                      >  1:3409161/1‑67 (MQ=255)
aaGATGTAAGCGAGCATTCACATCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGAGAATCt                                                      >  1:65444/1‑67 (MQ=255)
aaGATGTAAGCGAGCATTCACATCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGAGAATCt                                                      >  1:1618512/1‑67 (MQ=255)
     gTAAGCGAGCATTCACATCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGAGAATCTTTCAGCg                                               >  1:1906788/1‑69 (MQ=255)
     gTAAGCGAGCATTCACATCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGAGAATCTTTCAGCg                                               >  1:3065620/1‑69 (MQ=255)
     gTAAGCGAGCATTCACATCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGAGAATCTTTCAGCg                                               >  1:1519482/1‑69 (MQ=255)
     gTAAGCGAGCATTCACATCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGAGAATCTTTCAGCg                                               >  1:718031/1‑69 (MQ=255)
     gTAAGCGAGCATTCACATCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGAGAATCTTTCAGCg                                               >  1:1312114/1‑69 (MQ=255)
     gTAAGCGAGCATTCACATCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGAGAATCTTTCAGCg                                               >  1:929103/1‑69 (MQ=255)
      tAAGCGAGCATTCACATCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGAGAATCTTTCAGCgg                                              >  1:54982/1‑69 (MQ=255)
      tAAGCGAGCATTCACATCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGAGAATCTTTCAGCgg                                              >  1:415899/1‑69 (MQ=255)
      tAAGCGAGCATTCACATCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGAGAATCTTTCAGCgg                                              >  1:396872/1‑69 (MQ=255)
      tAAGCGAGCATTCACATCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGAGAATCTTTCAGCgg                                              >  1:658317/1‑69 (MQ=255)
      tAAGCGAGCATTCACATCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGAGAATCTTTCAGCgg                                              >  1:745877/1‑69 (MQ=255)
      tAAGCGAGCATTCACATCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGAGAATCTTTCAGCgg                                              >  1:2857591/1‑69 (MQ=255)
      tAAGCGAGCATTCACATCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGAGAATCTTTCAGCgg                                              >  1:1970635/1‑69 (MQ=255)
      tAAGCGAGCATTCACATCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGAGAATCTTTCAGCgg                                              >  1:2879436/1‑69 (MQ=255)
      tAAGCGAGCATTCACATCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGAGAATCTTTCAGCgg                                              >  1:1734616/1‑69 (MQ=255)
      tAAGCGAGCATTCACATCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGAGAATCTTTCAGCgg                                              >  1:1598710/1‑69 (MQ=255)
      tAAGCGAGCATTCACATCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGAGAATCTTTCAGCgg                                              >  1:1899941/1‑69 (MQ=255)
      tAAGCGAGCATTCACATCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGAGAATCTTTCAGCg                                               >  1:2288053/1‑68 (MQ=255)
      tAAGCGAGCATTCACATCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGAGAATCTTTCAGCg                                               >  1:2859185/1‑68 (MQ=255)
      tAAGCGAGCATTCACATCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGAGAATCTTTCAGCg                                               >  1:87206/1‑68 (MQ=255)
      tAAGCGAGCATTCACATCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGAGAATCTTTCAGCg                                               >  1:2032962/1‑68 (MQ=255)
      tAAGCGAGCATTCACATCGCCGTAGAGCTGGAGTTCTTGCAGGGTCGCACCCAGAGAATCTTTCAGCgg                                              >  1:2520529/1‑69 (MQ=255)
      tAAGCGAGCATTCACATCGCCGTAGAGCTGGAGTTCTTGCAGGGTCGCACCCAGAGAATCTTTCAGCg                                               >  1:2719508/1‑68 (MQ=255)
              cATTCACATCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGGTAATCTTTCAGCGGTGTCtca                                       >  1:2297375/1‑68 (MQ=255)
              cATTCACATCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGGGAATCTTTCAGCGGTGtctc                                        >  1:609100/1‑67 (MQ=255)
              cATTCACATCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGGGAATCTTTCAGCGGTGTCtca                                       >  1:1669088/1‑68 (MQ=255)
              cATTCACATCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGGGAATCTTTCAGCGGTGTCtca                                       >  1:1321503/1‑68 (MQ=255)
              cATTCACATCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGGGAATCTTTCAGCGGTGTCtca                                       >  1:3324567/1‑68 (MQ=255)
              cATTCACATCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGGGAATCTTTCAGCGGTGTCtca                                       >  1:1154617/1‑68 (MQ=255)
              cATTCACATCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGGGAATCTTTCAGCGGTGTCtca                                       >  1:1080916/1‑68 (MQ=255)
              cATTCACATCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGGGAATCTTTCAGCGGTGTCtca                                       >  1:3044427/1‑68 (MQ=255)
              cATTCACATCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGGGAATCTTTCAGCGGTGTCtca                                       >  1:1837230/1‑68 (MQ=255)
              cATTCACATCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGGGAATCTTTCAGCGGTGTCtca                                       >  1:467839/1‑68 (MQ=255)
              cATTCACATCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGGGAATCTTTCAGCGGTGTCtca                                       >  1:2522404/1‑68 (MQ=255)
              cATTCACATCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGGGAATCTTTCAGCGGTGTCtca                                       >  1:1879541/1‑68 (MQ=255)
              cATTCACATCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGGGAATCTTTCAGCGGTGTCtca                                       >  1:613055/1‑68 (MQ=255)
              cATTCACATCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGGGAATCTTTCAGCGGTGTCtca                                       >  1:1485411/1‑68 (MQ=255)
              cATTCACATCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGGGAATATTTCAGCGGTGTCtca                                       >  1:2160339/1‑68 (MQ=255)
                  cacaTCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGACAATCTTTCAGCgg                                              >  1:210251/1‑57 (MQ=255)
                     aTCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGGGAATCTTTCAGCGGTGTCTCATCAAAGTa                               <  1:435857/69‑1 (MQ=255)
                     aTCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGGGAATCTTTCAGCGGTGTCTCATCAAAGTa                               <  1:1884562/69‑1 (MQ=255)
                     aTCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGGGAATCTTTCAGCGGTGTCTCATCAAAGTa                               <  1:354381/69‑1 (MQ=255)
                     aTCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGGGAATCTTTCAGCGGTGTCTCATCAAAGTa                               <  1:1711751/69‑1 (MQ=255)
                     aTCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGGGAATCTTTCAGCGGTGTCTCATCAAAGTa                               <  1:3250606/69‑1 (MQ=255)
                     aTCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGGGAATCTTTCAGCGGTGTCTCATCAAAGTa                               <  1:1552570/69‑1 (MQ=255)
                     aTCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGGGAATCTTTCAGCGGTGTCTCATCAAAGTa                               <  1:303965/69‑1 (MQ=255)
                     aTCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGGGAATCTTTCAGCGGTGTCTCATCAAAGTa                               <  1:2145513/69‑1 (MQ=255)
                     aTCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGGGAATCTTTCAGCGGTGTCTCATCAAAGTa                               <  1:2371451/69‑1 (MQ=255)
                     aTCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGGGAATCTTTCAGCGGTGTCTCATCAAAGTa                               <  1:2857048/69‑1 (MQ=255)
                     aTCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGGGAATCTTTCAGCGGTGTCTCATCAAAGTa                               <  1:2895239/69‑1 (MQ=255)
                     aTCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGGGAATCTTTCAGCGGTGTCTCATCAAAGTa                               <  1:2899611/69‑1 (MQ=255)
                     aTCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGGGAATCTTTCAGCGGTGTCTCATCAAAGTa                               <  1:1812200/69‑1 (MQ=255)
                     aTCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGGGAATCTTTCAGCGGTGTCTCATCAAAGTa                               <  1:1751144/69‑1 (MQ=255)
                     aTCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGGGAATCTTTCAGCGGTGTCTCATCAAAGTa                               <  1:868993/69‑1 (MQ=255)
                     aTCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGAGAATCTTTCAGCGGTGTCTCATCAAAGt                                <  1:590010/68‑1 (MQ=255)
                      tCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGGGAATCTTTCAGCGGTGTCTCATCAAAGTa                               <  1:1671725/68‑1 (MQ=255)
                        gCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGAGAATCTTTCAGCGGTGTCtcatc                                     >  1:839247/1‑60 (MQ=255)
                        gCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGAGAATCTTTCAGCGGTGTCTCATCAAAGTAAgg                            >  1:1630893/1‑69 (MQ=255)
                        gCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGAGAATCTTTCAGCGGTGTCTCATCAAAGTAAgg                            >  1:895547/1‑69 (MQ=255)
                        gCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGAGAATCTTTCAGCGGTGTCTCATCAAAGTAAgg                            >  1:477449/1‑69 (MQ=255)
                        gCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGAGAATCTTTCAGCGGTGTCTCATCAAAGTAAgg                            >  1:3147899/1‑69 (MQ=255)
                        gCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGAGAATCTTTCAGCGGTGTCTCATCAAAGTAAgg                            >  1:2042199/1‑69 (MQ=255)
                          cGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGAGAATCTTTCAGCGGTGTCTCATCAAAGTAAggg                           >  1:980060/1‑68 (MQ=255)
                          cGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGAGAATCTTTCAGCGGTGTCTCATCAAAGTAAggg                           >  1:86751/1‑68 (MQ=255)
                          cGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGAGAATCTTTCAGCGGTGTCTCATCAAAGTAAggg                           >  1:1132542/1‑68 (MQ=255)
                          cGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGAGAATCTTTCAGCGGTGTCTCATCAAAGTAAggg                           >  1:1384536/1‑68 (MQ=255)
                          cGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGAGAATCTTTCAGCGGTGTCTCATCAAAGTAAggg                           >  1:294243/1‑68 (MQ=255)
                          cGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGAGAATCTTTCAGCGGTGTCTCATCAAAGTAAggg                           >  1:2806187/1‑68 (MQ=255)
                          cGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGAGAATCTTTCAGCGGTGTCTCATCAAAGTAAggg                           >  1:2523351/1‑68 (MQ=255)
                                 cTGGAGTTCTTGCAGGGTCGCACCCAGAGAATCTTTCAGCGGTGTCTCATCAAAGTAAGGGCCAACGGc                   <  1:3429333/69‑1 (MQ=255)
                                   tgAGTTCTTGCAGGGTCGCACCCAGGGTATCTTTCAGCGGTGTCTCATCAAAGTa                               <  1:1467668/54‑1 (MQ=255)
                                                ggTCGCACCCAGAGAATCTTTCAGCGGTGTCTCATCAAAGTAAGGGCCAACGGCTTTA‑CCCGGACCttt   <  1:1357034/69‑1 (MQ=255)
                                                ggTCGCACCCAGAGAATCTTTCAGCGGTGTCTCATCAAAGTAAGGGCCAACGGCTTTA‑CCCGGACCttt   <  1:3305669/69‑1 (MQ=255)
                                                ggTCGCACCCAGAGAATCTTTCAGCGGTGTCTCATCAAAGTAAGGGCCAACGGCTTTA‑CCCGGACCttt   <  1:2880501/69‑1 (MQ=255)
                                                ggTCGCACCCAGAGAATCTTTCAGCGGTGTCTCATCAAAGTAAGGGCCAACGGCTTTA‑CCCGGACCttt   <  1:911917/69‑1 (MQ=255)
                                                ggTCGCACCCAGAGAATCTTTCAGCGGTGTCTCATCAAAGTAAGGGCCAACGGCTTTA‑CCCGGACCttt   <  1:981523/69‑1 (MQ=255)
                                                 gTCGCACCCAGAGAATCTTTCAGCGGTGTCTCATCAAAGTAAGGGCCAACGGCTTTA‑CCCGGACCttt   <  1:921240/68‑1 (MQ=255)
                                                 gTCGCACCCAGAGAATCTTTCAGCGGTGTCTCATCAAAGTAAGGGCCAACGGCTTTA‑CCCGGACCTTTa  <  1:823336/69‑1 (MQ=255)
                                                 gTCGCACCCAGAGAATCTTTCAGCGGTGTCTCATCAAAGTAAGGGCCAACGGCTTTA‑CCCGGACCTTTa  <  1:2671187/69‑1 (MQ=255)
                                                 gTCGCACCCAGAGAATCTTTCAGCGGTGGCTCATCAAAGTAAGGGCCAACGGCTTTA‑CCCGGACCTTTa  <  1:1217012/69‑1 (MQ=255)
                                                  tCGCACCCAGAGAATCTTTCAGCGGTGTCTCATCAAAGTAAGGGCCAACGGCTTTACCCCGGACCTTTa  >  1:216536/1‑69 (MQ=255)
                                                            |                                                          
AAGATGTAAGCGAGCATTCACATCGCCGTCGAGCTGGAGTTCTTGCAGGGTCGCACCCAGAGAATCTTTCAGCGGTGTCTCATCAAAGTAAGGGCCAACGGCTTTA‑CCCGGACCTTTA  >  minE/2209540‑2209657

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