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 2,259,276 A→G 27.7% L623L (TTG→CTG)  rpoB ← RNA polymerase, beta subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,259,2760AG27.7% 186.3 / 77.3 173L623L (TTG→CTG) rpoBRNA polymerase, beta subunit
Reads supporting (aligned to +/- strand):  ref base A (73/52);  new base G (21/27);  total (94/79)
Fisher's exact test for biased strand distribution p-value = 9.10e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01

Only 100 of 173 total aligned reads displayed.

ACAAGCTGGATTCGCCTTTGCTACGGCAAGTTACCAGGTCTTCTACGAAGTGGCCTTCTTCATCCAAGTTGGAGTTCGCCTGGGCGATAACGTAGTTGCCTTCTTCGATAGCAGACAGGTAGTGAATTTCGTC  >  minE/2259210‑2259342
                                                                  |                                                                  
aCAAGCTGGATTCGCCTTTGCTACGGCAAGTTACCAGGTCTTCTACGAAGTGGCCTTCTTCATCCAAGt                                                                  >  1:164628/1‑69 (MQ=255)
aCAAGCTGGATTCGCCTTTGCTACGGCAAGTTACCAGGTCTTCTACGAAGTGGCCTTCTTCATCCAAGt                                                                  >  1:1835174/1‑69 (MQ=255)
aCAAGCTGGATTCGCCTTTGCTACGGCAAGTTAACAGGTCTTCTACGAAGTGGCCTTCTTCATCCAAGt                                                                  >  1:821919/1‑69 (MQ=255)
aCAAGCTGGATTCGCCTTTGCTACGGCAAGTTAACAGGTCTTCTACGAAGTGGCCTTCTTCATCCAAGt                                                                  >  1:1262736/1‑69 (MQ=255)
              ccTTTGCTACGGCAAGTTACCAGGTCTTCTACGAAGTGGCCTTCTTCATCCAAGTTGGAGTTCGCCTg                                                     <  1:1229284/68‑1 (MQ=255)
                      aCGGCAAGTTACCAGGTCTTCTACGAAGTGGCCTTCTTCATCCAAGTTGGAGTTCGCCTGGGCGATaa                                             <  1:3040028/68‑1 (MQ=255)
                      aCGGCAAGTTACCAGGTCTTCTACGAAGTGGCCTTCTTCATCCAAGTTGGAGTTCGCCTGGGCGATaa                                             <  1:113056/68‑1 (MQ=255)
                      aCGGCAAGTTACCAGGTCTTCTACGAAGTGGCCTTCTTCATCCAAGTTGGAGTTCGCCTGGGCGATaa                                             <  1:1156132/68‑1 (MQ=255)
                      aCGGCAAGTTACCAGGTCTTCTACGAAGTGGCCTTCTTCATCCAAGTTGGAGTTCGCCTGGGCGATaa                                             <  1:1762585/68‑1 (MQ=255)
                         gCAAGTTACCAGGTCTTCTACGAAGTGGCCTTCTTCATCCAAGTTGGAGTTCGCCTGGGCGATAACg                                           <  1:119570/67‑1 (MQ=255)
                         gCAAGTTACCAGGTCTTCTACGAAGTGGCCTTCTTCATCCAAGTTGGAGTTCGCCTGGGCGATAACg                                           <  1:2785594/67‑1 (MQ=255)
                         gCAAGTTACCAGGTCTTCTACGAAGTGGCCTTCTTCATCCAAGTTGGAGTTCGCCTGGGCGATAACg                                           <  1:1805867/67‑1 (MQ=255)
                         gCAAGTTACCAGGTCTTCTACGAAGTGGCCTTCTTCATCCAAGTTGGAGTTCGCCTGGGCGATAACg                                           <  1:2150275/67‑1 (MQ=255)
                         gCAAGTTACCAGGTCTTCTACGAAGTGGCCTTCTTCATCCAAGTTGGAGTTCGCCTGGGCGATAACGTa                                         <  1:1550073/69‑1 (MQ=255)
                         gCAAGTTACCAGGTCTTCTACGAAGTGGCCTTCTTCATCCAAGTTGGAGTTCGCCTGGGCGATAACGTa                                         <  1:1057932/69‑1 (MQ=255)
                         gCAAGTTACCAGGTCTTCTACGAAGTGGCCTTCTTCATCCAAGTTGGAGTTCGCCTGGGCGATAACGTa                                         <  1:2276581/69‑1 (MQ=255)
                         gCAAGTTACCAGGTCTTCTACGAAGTGGCCTTCTTCATCCAAGTTGGAGTTCGCCTGGGCGATAACGTa                                         <  1:2663219/69‑1 (MQ=255)
                         gCAAGTTACCAGGTCTTCTACGAAGTGGCCTTCTTCATCCAAGTTGGAGTTCGCCTGGGCGATAACGTa                                         <  1:2952600/69‑1 (MQ=255)
                         gCAAGTTACCAGGTCTTCTACGAAGTGGCCTTCTTCATCCAAGTTGGAGTTCGCCTGGGCGATAACGTa                                         <  1:989654/69‑1 (MQ=255)
                         gCAAGTTACCAGGTCTTCTACGAAGTGGCCTTCTTCATCCAAGTTGGAGTTCGCCTGGGCGATAACGTa                                         <  1:1474248/69‑1 (MQ=255)
                         gCAAGTTACCAGGTCTTCTACGAAGTGGCCTTCTTCATCCAAGTTGGAGTTCGCCTGGGCGATAACGTa                                         <  1:1534394/69‑1 (MQ=255)
                         gCAAGTTACCAGGTCTTCTACGAAGTGGCCTTCTTCATCCAAGTTGGAGTTCGCCTGGGCGATAACGTa                                         <  1:1117156/69‑1 (MQ=255)
                         gCAAGTTACCAGGTCTTCTACGAAGTGGCCTTCTTCATCCAAGTT‑GAGTTCGCCTGGGCGATAACGTa                                         <  1:601598/68‑1 (MQ=255)
                           aaGTTACCAGGTCTTCTACGAAGTGGCCTTCTTCATCCAAGTTGGAGTTCGccgg                                                     <  1:2595406/55‑3 (MQ=255)
                               tACCAGGTCTTCTACGAAGTGGCCTTCTTCATCCAGGTTGGAGtt                                                           >  1:201833/1‑45 (MQ=255)
                               tACCAGGTCTTCTACGAAGTGGCCTTCTTCATCCAGGTTGGAGTTCGCCTGGGCGATAACGt                                          >  1:2548647/1‑62 (MQ=255)
                               tACCAGGTCTTCTACGAAGTGGCCTTCTTCATCCAGGTTGGAGTTCGCCTGGGCGATAACGTa                                         >  1:2482373/1‑63 (MQ=255)
                               tACCAGGTCTTCTACGAAGTGGCCTTCTTCATCCAGGTTGGAGTTCGCCTGGGCGATAACGTa                                         >  1:2493574/1‑63 (MQ=255)
                               tACCAGGTCTTCTACGAAGTGGCCTTCTTCATCCAGGTTGGAGTTCGCCTGGGCGATAACGTa                                         >  1:2557462/1‑63 (MQ=255)
                               tACCAGGTCTTCTACGAAGTGGCCTTCTTCATCCAGGTTGGAGTTCGCCTGGGCGATAACGTa                                         >  1:1373826/1‑63 (MQ=255)
                               tACCAGGTCTTCTACGAAGTGGCCTTCTTCATCCAGGTTGGAGTTCGCCTGGGCGATAACGTa                                         >  1:2691177/1‑63 (MQ=255)
                               tACCAGGTCTTCTACGAAGTGGCCTTCTTCATCCAGGTTGGAGTTCGCCTGGGCGATAACGTa                                         >  1:2884511/1‑63 (MQ=255)
                               tACCAGGTCTTCTACGAAGTGGCCTTCTTCATCCAGGTTGGAGTTCGCCTGGGCGATAACGTa                                         >  1:3192783/1‑63 (MQ=255)
                               tACCAGGTCTTCTACGAAGTGGCCTTCTTCATCCAGGTTGGAGTTCGCCTGGGCGATAACGTa                                         >  1:3370389/1‑63 (MQ=255)
                               tACCAGGTCTTCTACGAAGTGGCCTTCTTCATCCAGGTTGGAGTTCGCCTGGGCGATAACGTa                                         >  1:791395/1‑63 (MQ=255)
                               tACCAGGTCTTCTACGAAGTGGCCTTCTTCATCCAGGTTGGAGTTCGCCTGGGCGATAACGTa                                         >  1:915931/1‑63 (MQ=255)
                               tACCAGGTCTTCTACGAAGTGGCCTTCTTCATCCAGGTTGGAGTTCGCCTGGGCGATAACGTa                                         >  1:946590/1‑63 (MQ=255)
                               tACCAGGTCTTCTACGAAGTGGCCTTCTTCATCCAGGTTGGAGTTCGCCTGGGCGATAAAGTa                                         >  1:2717345/1‑63 (MQ=255)
                               tACCAGGTCTTCTACGAAGTGGCCTTCTTCATCCAGGTTGGAGTTCGCCTGGGAGATAACGTa                                         >  1:1491110/1‑63 (MQ=255)
                               tACCAGGTCTTCTACGAAGTGGCCTTCTTCATCCAGGTTGGAGTTCGACTGGGCGATAACGTa                                         >  1:2453049/1‑63 (MQ=255)
                               tACCAGGTCTTCTACGAAGTGGCCTTCTTCATCCAAGTTGGAGTTCGCCTGGGCGATAACGTAGTTGcc                                   >  1:2949942/1‑69 (MQ=255)
                               tACCAGGTCTTCTACGAAGTGGCCTTCTTCATCCAAGTTGGAGTTCGCCTGGGCGATAACGTAGTTGcc                                   >  1:3411550/1‑69 (MQ=255)
                               tACCAGGTCTTCTACGAAGTGGCCTTCTTCATCCAAGTTGGAGTTCGCCTGGGCGATAACGTAGTTGcc                                   >  1:556714/1‑69 (MQ=255)
                               tACCAGGTCTTCTACGAAGTGGCCTTCTTCATCCAAGTTGGAGTTCGCCTGGGCGATAACGTAGTTGcc                                   >  1:2630536/1‑69 (MQ=255)
                               tACCAGGTCTTCTACGAAGTGGCCTTCTTCATCCAAGTTGGAGTTCGCCTGGGCGATAACGTAGTTGcc                                   >  1:967176/1‑69 (MQ=255)
                               tACCAGGTCTTCTACGAAGTGGCCTTCTTCATCCAAGTTGGAGTTCGCCTGGGCGATAACGTAGTTGc                                    >  1:779280/1‑68 (MQ=255)
                                          ctAGGAAGTGGCCTTCTTCATCCAAGTTGGAGTTCGCCTGGGCGATAACGTAGTTGCCttcttc                             >  1:1201223/1‑64 (MQ=255)
                                          ctACGAAGTGGCCTTCTTCATCCAAGTTGGAGTTCGCCTGGGCGATAACGTAGTTGCCttcttc                             >  1:2244631/1‑64 (MQ=255)
                                          ctACGAAGTGGCCTTCTTCATCCAAGTTGGAGTTCGCCTGGGCGATAACGTAGTTGCCttcttc                             >  1:2938073/1‑64 (MQ=255)
                                          ctACGAAGTGGCCTTCTTCATCCAAGTTGGAGTTCGCCTGGGCGATAACGTAGTTGCCttcttc                             >  1:2968995/1‑64 (MQ=255)
                                          ctACGAAGTGGCCTTCTTCATCCAAGTTGGAGTTCGCCTGGGCGATAACGTAGTTGCCttcttc                             >  1:1955453/1‑64 (MQ=255)
                                          ctACGAAGTGGCCTTCTTCATCCAAGTTGGAGTTCGCCTGGGCGATAACGTAGTTGCCttcttc                             >  1:146214/1‑64 (MQ=255)
                                          ctACGAAGTGGCCTTCTTCATCCAAGTTGGAGTTCGCCTGGGCGATAACGTAGTTGCCttcttc                             >  1:3069378/1‑64 (MQ=255)
                                          ctACGAAGTGGCCTTCTTCATCCAAGTTGGAGTTCGCCTGGGCGATAACGTAGTTGCCttcttc                             >  1:934162/1‑64 (MQ=255)
                                          ctACGAAGTGGCCTTCTTCATCCAAGTTGGAGTTCGCCTGGGCGATAACGTAGTTGCCttcttc                             >  1:1375412/1‑64 (MQ=255)
                                          ctACGAAGTGGCCTTCTTCATCCAAGTTGGAGTTCGCCTGGGCGATAACGTAGTTGCCttcttc                             >  1:3330772/1‑64 (MQ=255)
                                          ctACGAAGTGGCCTTCTTCATCCAAGTTGGAGTTCGCCTGGGCGATAACGTAGTTGCCttcttc                             >  1:2335793/1‑64 (MQ=255)
                                          ctACGAAGTGGCCTTCTTCATCCAAGTTGGAGTTCGCCTGGGCGATAACGTAGTTGCCttcttc                             >  1:1627822/1‑64 (MQ=255)
                                          ctACGAAGTGGCCTTCTTCATCCAAGTTGGAGTTCGCCTGGGCGATAACGTAGTTGCCttcttc                             >  1:1860880/1‑64 (MQ=255)
                                          ctACGAAGTGGCCTTCTTCAGCCAAGTTGGAGTTCGCCTGGGCGATAACGTAGTTGCCttcttc                             >  1:3127418/1‑64 (MQ=255)
                                           tACGAAGTGGCCTTCTTCATCCAAGTTGGAGTTCGCCTGGGCGATAACGt                                          >  1:2280215/1‑50 (MQ=255)
                                           tACGAAGTGGCCTTCTTCATCCAAGTTGGAGTTCGCCTGGGCGATAACGTAGTTGCCTTCTTCGa                           >  1:2608530/1‑65 (MQ=255)
                                           tACGAAGTGGCCTTCTTCATCCAAGTTGGAGTTCGCCTGGGCGATAACGTAGTTGCCTTCTTCGAt                          >  1:2903101/1‑66 (MQ=255)
                                           tACGAAGTGGCCTTCTTCATCCAAGTTGGAGTTCGCCTGGGCGATAACGTAGTTGCCTTCTTCGAt                          >  1:1448917/1‑66 (MQ=255)
                                           tACGAAGTGGCCTTCTTCATCCAAGTTGGAGTTCGCCTGGGCGATAACGTAGTTGCCTTCTTCGAt                          >  1:611730/1‑66 (MQ=255)
                                           tACGAAGTGGCCTTCTTCATCCAAGTTGGAGTTCGCCTGGGCGATAACGTAGTTGCCTTCTTCGAt                          >  1:1790143/1‑66 (MQ=255)
                                           tACGAAGTGGCCTTCTTCATCCAAGTTGGAGTTCGCCTGGGCGATAACGTAGTTGCCTTCTTCGAt                          >  1:2225828/1‑66 (MQ=255)
                                           tACGAAGTGGCCTTCTTCATCCAAGTTGGAGTTCGCCTGGGCGATAACGTAGTTGCCTTCTTCGAt                          >  1:2568700/1‑66 (MQ=255)
                                           tACGAAGTGGCATTCTTCATCCAAGTTGGAGTTCGCCTGGGCGATAACGTAGTTGCCTTCTTCGAt                          >  1:2585480/1‑66 (MQ=255)
                                            aCGAAGTGGCCTTCTTCATCCAGGTTGGAGTTCGCCTGGGCGATAACGTAGTTGCCTTCTTCGATa                         <  1:643642/66‑1 (MQ=255)
                                            aCGAAGTGGCCTTCTTCATCCAGGTTGGAGTTCGCCTGGGCGATAACGTAGTTGCCTTCTTCGATa                         <  1:212774/66‑1 (MQ=255)
                                            aCGAAGTGGCCTTCTTCATCCAGGTTGGAGTTCGCCTGGGCGATAACGTAGTTGCCTTCTTCGATa                         <  1:317660/66‑1 (MQ=255)
                                            aCGAAGTGGCCTTCTTCATCCAGGTTGGAGTTCGCCTGGGCGATAACGTAGTTGCCTTCTTCGATa                         <  1:3213389/66‑1 (MQ=255)
                                            aCGAAGTGGCCTTCTTCATCCAGGTTGGAGTTCGCCTGGGCGATAACGTAGTTGCCTTCTTCGATa                         <  1:3278828/66‑1 (MQ=255)
                                            aCGAAGTGGCCTTCTTCATCCAGGTTGGAGTTCGCCTGGGCGATAACGTAGTTGCCTTCTTCGATa                         <  1:2530056/66‑1 (MQ=255)
                                               aaGTGGCCTTCTTCATCCAGGTTGGAGTTCGCCTGGGCGATAACGTAGTTGCCTTCTTCGATAGCAGa                    <  1:652018/68‑1 (MQ=255)
                                               aaGTGGCCTTCTTCATCCAGGTTGGAGTTCGCCTGGGCGATAACGTAGTTGCCTTCTTCGATAGCAGa                    <  1:1055293/68‑1 (MQ=255)
                                               aaGTGGCCTTCTTCATCCAGGTTGGAGTTCGCCTGGGCGATAACGTAGTTGCCTTCTTCGATAGCAGa                    <  1:1705606/68‑1 (MQ=255)
                                               aaGTGGCCTTCTTCATCCAGGTTGGAGTTCGCCTGGGCGATAACGTAGTTGCCTTCTTCGATAGCAGa                    <  1:408772/68‑1 (MQ=255)
                                               aaGTGGCCTTCTTCATCCAGGTTGGAGTTCGCCTGGGCGATAACGTAGTTGCCTTCTTCGATAGCAGa                    <  1:2400692/68‑1 (MQ=255)
                                               aaGTGGCCTTCTTCATCCAGGTTGGAGTTCGCCTGGGCGATAACGTAGTTGCCTTCTTCGATAGCAGa                    <  1:3197338/68‑1 (MQ=255)
                                               aaGTGGCCTTCTTCATCCAGGTTGGAGTTCGCCTGGGCGATAACGTAGTTGCCTTCTTCGATAGCAGa                    <  1:2792900/68‑1 (MQ=255)
                                               aaGTGGCCTTCTTCATCCAGGTTGGAGTTCGCCTGGGCGATAACGTAGTTGCCTTCTTCGATAGCAGa                    <  1:2797949/68‑1 (MQ=255)
                                               aaGTGGCCTTCTTCATCCAAGTTGGAGTTCGCCTGGGCGATAACGTAGTTGCCTTCTTCGATAGCAGAc                   <  1:1573357/69‑1 (MQ=255)
                                                aGTGGCCTTCTTCATCCAAGTTGGAGTTCGCCTGGGCGATAACGTAGTTGCCTTCTTCGATAGCAGAc                   <  1:2022359/68‑1 (MQ=255)
                                                aGTGGCCTTCTTCATCCAAGTTGGAGTTCGCCTGGGCGATAACGTAGTTGCCTTCTTCGATAGCAGACa                  <  1:3415605/69‑1 (MQ=255)
                                                aGTGGCCTTCTTCATCCAAGTTGGAGTTCGCCTGGGCGATAACGTAGTTGCCTTCTTCGATAGCAGACa                  <  1:840419/69‑1 (MQ=255)
                                                aGTGGCCTTCTTCATCCAAGTTGGAGTTCGCCTGGGCGATAACGTAGTTGCCTTCTTCGATAGCAGACa                  <  1:2929988/69‑1 (MQ=255)
                                                aGTGGCCTTCTTCATCCAAGTTGGAGTTCGCCTGGGCGATAACGTAGTTGCCTTCTTCGATAGCAGACa                  <  1:1432637/69‑1 (MQ=255)
                                                    gCCTTCTTCATCCAAGTTGGAGTTCGCCTGGGCGATAACGTAGTTGCCTTCTTCGATAGCAGACAGGTa              >  1:1135223/1‑69 (MQ=255)
                                                     ccTTCTTCATCCAAGTTGGAGTTCGCCTGGGCGATaa                                             <  1:68605/37‑1 (MQ=255)
                                                       ttcttcATCCAAGTTGGAGTTCGCCTGGTCGATTACGTAGTTGCCTTCTTCGATAGCAGACAGGTAGTg           <  1:489003/69‑1 (MQ=255)
                                                       ttcttcATCCAAGTTGGAGTTCGCCTGGGCGATAACGTAGTTGCCTTCTTCGATAGAAGACAGGTAGTg           <  1:2205676/69‑1 (MQ=255)
                                                            cATCCAAGTTGGAGTTCGCCTGGGCGATAACGTAGTTGCCttcttc                             >  1:1870798/1‑46 (MQ=255)
                                                            cATCCAAGTTGGAGTTCGCCTGGGCGATAACGTAGTTGCCttcttc                             >  1:94879/1‑46 (MQ=255)
                                                            cATCCAAGTTGGAGTTCGCCTGGGCGATAACGTAGTTGCCttcttc                             >  1:2440743/1‑46 (MQ=255)
                                                            cATCCAAGTTGGAGTTCGCCTGGGCGATAACGTAGTTGCCttcttc                             >  1:1383602/1‑46 (MQ=255)
                                                            cATCCAAGTTGGAGTTCGCCTGGGCGATAACGTAGTTGCCttcttc                             >  1:1066781/1‑46 (MQ=255)
                                                            cATCCAAGTTGGAGTTCGCCTGGGCGATAACGTAGTTGCCttcttc                             >  1:1904598/1‑46 (MQ=255)
                                                                cAAGTTGGAGTTCGCCTGGGCGATAACGTAGTTGCCTTCTTCGATAGCAGACAGGTAGTGATTTTCGTc  >  1:691523/1‑69 (MQ=255)
                                                                  |                                                                  
ACAAGCTGGATTCGCCTTTGCTACGGCAAGTTACCAGGTCTTCTACGAAGTGGCCTTCTTCATCCAAGTTGGAGTTCGCCTGGGCGATAACGTAGTTGCCTTCTTCGATAGCAGACAGGTAGTGAATTTCGTC  >  minE/2259210‑2259342

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