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 1,605,751 T→G 31.1% L114L (CTT→CTG)  amiA → N‑acetylmuramoyl‑l‑alanine amidase I

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,605,7510TG31.1% 162.0 / 118.5 164L114L (CTT→CTG) amiAN‑acetylmuramoyl‑l‑alanine amidase I
Reads supporting (aligned to +/- strand):  ref base T (52/61);  new base G (15/36);  total (67/97)
Fisher's exact test for biased strand distribution p-value = 5.89e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.32e-01

Only 100 of 166 total aligned reads displayed.

CCATTTTGCGTAATCATGGGATTGATGCGCGTTTAACGCGTTCTGGCGATACGTTTATCCCACTTTACGATCGCGTTGAAATCGCCCATAAACATGGCGCAGATCTGTTTATGTCAATTCATGCC  >  minE/1605687‑1605811
                                                                |                                                            
ccATTTTGCGTAATCATGGGATTGATGCGCGTTTAACGCGTTCTGGCGATACGTTTATCCCACTTTACg                                                          >  1:1757199/1‑69 (MQ=255)
ccATTTTGCGTAATCATGGGATTGATGCGCGTTTAACGCGTTCTGGCGATACGTTTATCCCACTTTACg                                                          >  1:1631938/1‑69 (MQ=255)
ccATTTTGCGTAATCATGGGATTGATGCGCGTTTAACGCGTTCTGGCGATACGTTTATCCCACTTTACg                                                          >  1:445221/1‑69 (MQ=255)
ccATTTTGCGTAATCATGGGATTGATGCGCGTTTAACGCGTTCTGGCGATACGTTTATCCCACTTTACg                                                          >  1:946872/1‑69 (MQ=255)
     ttGCGTAATCATGGGATTGATGCGCGTTTAACGCGTTCTGGCGATACGTTTATCCCACTTTACGATcgc                                                     >  1:558897/1‑69 (MQ=255)
     ttGCGTAATCATGGGATTGATGCGCGTTTAACGCGTTCTGGCGATACGTTTATCCCACTTTACGATcgc                                                     >  1:252079/1‑69 (MQ=255)
     ttGCGTAATCATGGGATTGATGCGCGTTTAACGCGTTCTGGCGATACGTTTATCCCACTTTACGATcgc                                                     >  1:108838/1‑69 (MQ=255)
     ttGCGTAATCATGGGATTGATGCGCGTTTAACGCGTTCTGGCGATACGTTTATCCCACTTTACGATcgc                                                     >  1:308292/1‑69 (MQ=255)
     ttGCGTAATCATGGGATTGATGCGCGTTTAACGCGTTCTGGCGATACGTTTATCCCACTTTACGATcgc                                                     >  1:1807487/1‑69 (MQ=255)
     ttGCGTAATCATGGGATTGATGCGCGTTTAACGCGTTCTGGCGATACGTTTATCCCACTTTACGATcgc                                                     >  1:1755057/1‑69 (MQ=255)
     ttGCGTAATCATGGGATTGATGCGCGTTTAACGCGTTCTGGCGATACGTTTATCCCACTTTACGATcgc                                                     >  1:3305668/1‑69 (MQ=255)
     ttGCGTAATCATGGGATTGATGCGCGTTTAACGCGTTCTGGCGATACGTTTATCCCACTTTACAATcgc                                                     >  1:1019781/1‑69 (MQ=255)
              cATGGCATTGATGCGCGTTTAACGCGTTCTGGCGATACGTTTATCCCACTGTACGATCGCGTGGAAATc                                            <  1:1577198/69‑1 (MQ=255)
              cATGGCATTGATGCGCGTTTAACGCGTTCTGGCGATACGTTTATCCCACTGTACGATCGCGTGGAAATc                                            <  1:1849381/69‑1 (MQ=255)
              cATGGCATTGATGCGCGTTTAACGCGTTCTGGCGATACGTTTATCCCACTGTACGATCGCGTGGAAATc                                            <  1:742394/69‑1 (MQ=255)
              cATGGCATTGATGCGCGTTTAACGCGTTCTGGCGATACGTTTATCCCACTGTACGATCGCGTGGAAATc                                            <  1:1796158/69‑1 (MQ=255)
              cATGGCATTGATGCGCGTTTAACGCGTTCTGGCGATACGTTTATCCCACTGTACGATCGCGTGGAAATc                                            <  1:3068621/69‑1 (MQ=255)
              cATGGCATTGATGCGCGTTTAACGCGTTCTGGCGATACGTTTATCCCACTGTACGATCGCGTGGAAATc                                            <  1:2951836/69‑1 (MQ=255)
              cATGGCATTGATGCGCGTTTAACGCGTTCTGGCGATACGTTTATCCCACTGTACGATCGCGTGGAAATc                                            <  1:3425678/69‑1 (MQ=255)
              cATGGCATTGATGCGCGTTTAACGCGTTCTGGCGATACGTTTATCCCACTGTACGATCGCGTGGAAATc                                            <  1:286459/69‑1 (MQ=255)
              cATGGCATTGATGCGCGTTTAACGCGTTCTGGCGATACGTTTATCCCACTGTACGATCGCGTGGAAATc                                            <  1:283151/69‑1 (MQ=255)
              cATGGCATTGATGCGCGTTTAACGCGTTCTGGCGATACGTTTATCCCACTGTACGATCGCGTGGAAATc                                            <  1:2742745/69‑1 (MQ=255)
              cATGGCATTGATGCGCGTTTAACGCGTTCTGGCGATACGTTTATCCCACTGTACGATCGCGTGGAAATc                                            <  1:3265350/69‑1 (MQ=255)
              cATGGCATTGATGCGCGTTTAACGCGTTCTGGCGATACGTTTATCCCACTGTACGATCGCGTGGAAATc                                            <  1:2292436/69‑1 (MQ=255)
              cATGGCATTGATGCGCGTTTAACGCGTTCTGGCGATACGTTTATCCCACTGTACGATCGCGTGGAAATc                                            <  1:234094/69‑1 (MQ=255)
              cATGGCATTGATGCGCGTTTAACGCGTTCTGGCGATACGTTTATCCCACTGTACGATCGCGTGGAAATc                                            <  1:1290072/69‑1 (MQ=255)
              cATGGCATTGATGCGCGTTTAACGCGTTCTGGCGATACGTTTATCCCACTGTACGATCGCGTGGAAATc                                            <  1:254728/69‑1 (MQ=255)
              cATGGCATTGATGCGCGTTTAACGCGTTCTGGCGATACGTTTATCCCACTGTACGATCGCGTGGAAATc                                            <  1:1292358/69‑1 (MQ=255)
              cATGGCATTGATGCGCGTTTAACGCGTTCTGGCGATACGTTTATCCCACTGTACGATCGCGTGGAAATc                                            <  1:1296455/69‑1 (MQ=255)
              cATGGCATTGATGCGCGTTTAACGCGTTCTGGCGATACGTTTATCCCACTGTACGATCGCGTGGAAATc                                            <  1:130293/69‑1 (MQ=255)
                    aTTGATGCGCGTTTAACGCGTTCTGGCGATACGTTTATCCCACTGTACGATCGCGTGGAAATCGCCCa                                       <  1:512797/68‑1 (MQ=255)
                    aTTGATGCGCGTTTAACGCGTTCTGGCGATACGTTTATCCCACTGTACGATCGCGTGGAAATCGCCCa                                       <  1:2191593/68‑1 (MQ=255)
                    aTTGATGCGCGTTTAACGCGTTCTGGCGATACGTTTATCCCACTGTACGATCGCGTGGAAATCGCCCa                                       <  1:3123911/68‑1 (MQ=255)
                    aTTGATGCGCGTTTAACGCGTTCTGGCGATACGTTTATCCCACTGTACGATCGCGTGGAAATCGCCCa                                       <  1:1010726/68‑1 (MQ=255)
                    aTTGATGCGCGTTTAACGCGTTCTGGCGATACGTTTATCCCACTGTACGATCGCGTGGAAATCGCCCa                                       <  1:1785754/68‑1 (MQ=255)
                    aTTGATGCGCGTTTAACGCGTTCTGGCGATACGTTTATCCCACTGTACGATCGCGTGGAAATCGCCCa                                       <  1:1167114/68‑1 (MQ=255)
                       gATGCGCGTTTAACGCGTTCTGGCGATACGTTTATCCCACTTTACGATCGCGTTGAAATCGCCCATaaa                                   <  1:1146063/69‑1 (MQ=255)
                       gATGCGCGTTTAACGCGTTCTGGCGATACGTTTATCCCACTTTACGATCGCGTTGAAATCGCCCATaaa                                   <  1:2139864/69‑1 (MQ=255)
                       gATGCGCGTTTAACGCGTTCTGGCGATACGTTTATCCCACTTTACGATCGCGTTGAAATCGCCCATaaa                                   <  1:2629389/69‑1 (MQ=255)
                       gATGCGCGTTTAACGCGTTCTGGCGATACGTTTATCCCACTGTACGATCGCGTGGAAATCGCCCa                                       <  1:2644099/65‑1 (MQ=255)
                        aTGCGCGTTTAACGCGTTCTGGCGATACGTTTATCCCACTTTACGATCGCGTTGAAATCGCCCATaaa                                   <  1:1397093/68‑1 (MQ=255)
                        aTGCGCGTTTAACGCGTTCTGGCGATACGTTTATCCCACTTTACGATCGCGTTGAAATCGCCCATaaa                                   <  1:274200/68‑1 (MQ=255)
                         tGCGCGTTTAACGCGTTCTGGCGATACGTTTATCCCACTTTACGATCGCGTTGAAATCGCCCATaaa                                   <  1:870916/67‑1 (MQ=255)
                         tGCGCGTTTAACGCGTTCTGGCGATACGTTTATCCCACTTTACGATCGCGTTGAAATCGCCCATaaa                                   <  1:148693/67‑1 (MQ=255)
                         tGCGCGTTTAACGCGTTCTGGCGATACGTTTATCCCACTTTACGATCGCGTTGAAATCGCCCATaaa                                   <  1:1087127/67‑1 (MQ=255)
                         tGCGCGTTTAACGCGTTCTGGCGATACGTTTATCCCACTTTACGATCGCGTTGAAATCGCCCATaaa                                   <  1:1273074/67‑1 (MQ=255)
                         tGCGCGTTTAACGCGTTCTGGCGATACGTTTATCCCACTTTACGATCGCGTTGAAATCGCCCATaaa                                   <  1:501148/67‑1 (MQ=255)
                              gTTTAACGCGTTCTGGCGATACGTTTATCCCACTTTACGATCGCGTTGAAATCGCCCATAAACATGgcg                            <  1:1597699/69‑1 (MQ=255)
                                 tAACGCGTTCTGGCGATACGTTTATCCCACTTTACGATCGCGTTGAAATCGCCCATAAACATgg                              >  1:1090221/1‑64 (MQ=255)
                                 tAACGCGTTCTGGCGATACGTTTATCCCACTTTACGATCGCGTTGAAATCGCCCATAAACATgg                              >  1:2436349/1‑64 (MQ=255)
                                 tAACGCGTTCTGGCGATACGTTTATCCCACTTTACGATCGCGTTGAAATCGCCCATAAACATgg                              >  1:2351415/1‑64 (MQ=255)
                                 tAACGCGTTCTGGCGATACGTTTATCCCACTTTACGATCGCGTTGAAATCGCCCATAAACATgg                              >  1:2303292/1‑64 (MQ=255)
                                 tAACGCGTTCTGGCGATACGTTTATCCCACTTTACGATCGCGTTGAAATCGCCCATAAACATGGCGCAg                         >  1:3150670/1‑69 (MQ=255)
                                  aaCGCGTTCTGGCGATACGTTTATCCCACTTTACg                                                          >  1:409044/1‑35 (MQ=255)
                                  aaCGCGTTCTGGCGATACGTTTATCCCACTTTACg                                                          >  1:3391264/1‑35 (MQ=255)
                                  aaCGCGTTCTGGCGATACGTTTATCCCACTTTACg                                                          >  1:1316367/1‑35 (MQ=255)
                                  aaCGCGTTCTGGCGATACGTTTATCCCACTTTACg                                                          >  1:938864/1‑35 (MQ=255)
                                  aaCGCGTTCTGGCGATACGTTTATCCCACTTTACg                                                          >  1:2268794/1‑35 (MQ=255)
                                  aaCGCGTTCTGGCGATACGTTTATCCCACTTTACg                                                          >  1:2226477/1‑35 (MQ=255)
                                        ttCTGGCGATACGTTTATCCCACTTTACGATCGCGTTGAAATCGCCCATAAACATGGCGCAGATCTGtt                  >  1:2482056/1‑69 (MQ=255)
                                        ttCTGGCGATACGTTTATCCCACTTTACGATCGCGTTGAAATCGCCCATAAACATGGCGCAGATCTGtt                  >  1:1247453/1‑69 (MQ=255)
                                        ttCTGGCGATACGTTTATCCCACTTTACGATCGCGTTGAAATCGCCCATAAACATGGCGCAGATCTGtt                  <  1:3334399/69‑1 (MQ=255)
                                        ttCTGGCGATACGTTTATCCCACTTTACGATCGCGTTGAAATCGCCCATAAACATGGCGCAGATCTGtt                  <  1:1496762/69‑1 (MQ=255)
                                        ttCTGGCGATACGTTTATCCCACTTTACGATCGCGTTGAAATCGCCCATAAACATGGCGCAGATCTGtt                  >  1:3224015/1‑69 (MQ=255)
                                        ttCTGGCGATACGTTTATCCCACTTTACGATCGCGTTGAAATCGCCCATAAACATGGCGCAGATCTGtt                  <  1:3214388/69‑1 (MQ=255)
                                        ttCTGGCGATACGTTTATCCCACTTTACGATCGCGTTGAAATCGCCCATAAACATGGCGCAGATCTGtt                  <  1:3210424/69‑1 (MQ=255)
                                        ttCTGGCGATACGTTTATCCCACTTTACGATCGCGTTGAAATCGCCCATAAACATGGCGCAGATCTGtt                  <  1:1542277/69‑1 (MQ=255)
                                        ttCTGGCGATACGTTTATCCCACTTTACGATCGCGTTGAAATCGCCCATAAACATGGCGCAGATCTGtt                  >  1:1932207/1‑69 (MQ=255)
                                        ttCTGGCGATACGTTTATCCCACTTTACGATCGCGTTGAAATCGCCCATAAACATGGCGCAGATCTGtt                  >  1:2023591/1‑69 (MQ=255)
                                        ttCTGGCGATACGTTTATCCCACTTTACGATCGCGTTGAAATCGCCCATAAACATGGCGCAGATCTGtt                  <  1:2083035/69‑1 (MQ=255)
                                        ttCTGGCGATACGTTTATCCCACTTTACGATCGCGTTGAAATCGCCCATAAACATGGCGCAGATCTGtt                  <  1:2274470/69‑1 (MQ=255)
                                        ttCTGGCGATACGTTTATCCCACTTTACGATCGCGTTGAAATCGCCCATAAACATGGCGCAGATCTGtt                  <  1:628110/69‑1 (MQ=255)
                                        ttCTGGCGATACGTTTATCCCACTTTACGATCGCGTTGAAATCGCCCATAAACATGGCGCAGATCTGtt                  <  1:568769/69‑1 (MQ=255)
                                         tCTGGCGATACGTTTATCCCACTTTACGATCGCGTTGAAATCGCCCATAAACATGGCGCAGATCTGtt                  <  1:2754789/68‑1 (MQ=255)
                                         tCTGGCGATACGTTTATCCCACTTTACGATCGCGTTGAAATCGCCCATAAACATGGCGCAGATCTGtt                  <  1:901190/68‑1 (MQ=255)
                                                     tttATCCCACTGTACGATCGCGTGGAAATCGCCCATAAACACGGCGCAGACCTGTTTATGTCAATTCac     >  1:701412/1‑68 (MQ=255)
                                                     tttATCCCACTGTACGATCGCGTGGAAATCGCCCATAAACACGGCGCAGACCTGTTTATGTCAATTCac     >  1:462733/1‑68 (MQ=255)
                                                     tttATCCCACTGTACGATCGCGTGGAAATCGCCCATAAACACGGCGCAGACCTGTTTATGTCAATTCac     >  1:498261/1‑68 (MQ=255)
                                                     tttATCCCACTGTACGATCGCGTGGAAATCGCCCATAAACACGGCGCAGACCTGTTTATGTCAATTCac     >  1:67483/1‑68 (MQ=255)
                                                     tttATCCCACTGTACGATCGCGTGGAAATCGCCCATAAACACGGCGCAGACCTGTTTATGTCAATTCac     >  1:977726/1‑68 (MQ=255)
                                                     tttATCCCACTGTACGATCGCGTGGAAATCGCCCATAAACACGGCGCAGACCTGTTTATGTCAATTCac     >  1:1408212/1‑68 (MQ=255)
                                                     tttATCCCACTGTACGATCGCGTGGAAATCGCCCATAAACACGGCGCAGACCTGTTTATGTCAATTCac     >  1:2796265/1‑68 (MQ=255)
                                                     tttATCCCACTGTACGATCGCGTGGAAATCGCCCATAAACACGGCGCAGACCTGTTTATGTCAATTCac     >  1:2566684/1‑68 (MQ=255)
                                                     tttATCCCACTGTACGATCGCGTGGAAATCGCCCATAAACACGGCGCAGACCTGTTTATGTCAATTCac     >  1:1587072/1‑68 (MQ=255)
                                                     tttATCCCACTGTACGATCGCGTGGAAATCGCCCATAAACACGGCGCAGACCTGTTTATGTCAATTCac     >  1:2353333/1‑68 (MQ=255)
                                                       taacccACTTTACGATCGCGTTGAAATCGCCCATAAACATGGCGCAGATCTGTTTATGTCAATTCATg    >  1:2555619/4‑68 (MQ=255)
                                                       tATCCTACTTTACGATCGCGTTGAAATCGCCCATAAACATGGCGCAGATCTGTTTATGTCaa          <  1:2499350/62‑1 (MQ=255)
                                                       tATCCCACTTTACGATCGCGTTGAAATCGCCCATAAACATGGCGCAGATCTGtt                  >  1:1111890/1‑54 (MQ=255)
                                                       tATCCCACTTTACGATCGCGTTGAAATCGCCCATAAACATGGCGCAGATCTGtt                  >  1:1319736/1‑54 (MQ=255)
                                                       tATCCCACTTTACGATCGCGTTGAAATCGCCCATAAACATGGCGCAGATCTGtt                  >  1:2658287/1‑54 (MQ=255)
                                                       tATCCCACTTTACGATCGCGTTGAAATCGCCCATAAACATGGCGCAGATCTGt                   >  1:2919258/1‑53 (MQ=255)
                                                       tATCCCACTTTACGATCGCGTTGAAATCGCCCATAAACATGGCGCAGATCTGTTTATGTCaa          <  1:2447629/62‑1 (MQ=255)
                                                       tATCCCACTTTACGATCGCGTTGAAATCGCCCATAAACATGGCGCAGATCTGTTTATGTCAATTCATg    >  1:2070538/1‑68 (MQ=255)
                                                       tATCCCACTTTACGATCGCGTTGAAATCGCCCATAAACATGGCGCAGATCTGTTTATGTCAATTCATg    >  1:482195/1‑68 (MQ=255)
                                                       tATCCCACTTTACGATCGCGTTGAAATCGCCCATAAACATGGCGCAGATCTGTTTATGTCAATTCATg    >  1:475762/1‑68 (MQ=255)
                                                       tATCCCACTTTACGATCGCCTTGAAATCGCCCATAAACATGGCGCAGATc                      >  1:1427936/1‑50 (MQ=255)
                                                         tCCCACTTTACGATCGCGTTGAAATCGCCCATAAACATGGCGCAGATCTGTTTATGTCAATTCATGcc  <  1:1811357/68‑1 (MQ=255)
                                                         tCCCACTTTACGATCGCGTTGAAATCGCCCATAAACATGGCGCAGATCTGTTTATGTCAATTCATGcc  <  1:338006/68‑1 (MQ=255)
                                                         tCCCACTTTACGATCGCGTTGAAATCGCCCATAAACATGGCGCAGATCTGTTTATGTCAATTCATGcc  <  1:453587/68‑1 (MQ=255)
                                                                ttACGATCGCGTTGAAATCGCCCATAAACATGGCGCAGATCTGtt                  <  1:927004/45‑1 (MQ=255)
                                                                |                                                            
CCATTTTGCGTAATCATGGGATTGATGCGCGTTTAACGCGTTCTGGCGATACGTTTATCCCACTTTACGATCGCGTTGAAATCGCCCATAAACATGGCGCAGATCTGTTTATGTCAATTCATGCC  >  minE/1605687‑1605811

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A