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 1,625,969 C→T 39.3% N22N (AAC→AAT)  tktB → transketolase 2, thiamin‑binding

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,625,9690CT39.3% 80.9 / 102.6 150N22N (AAC→AAT) tktBtransketolase 2, thiamin‑binding
Reads supporting (aligned to +/- strand):  ref base C (50/41);  new base T (41/18);  total (91/59)
Fisher's exact test for biased strand distribution p-value = 8.82e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 152 total aligned reads displayed.

TGTCCCGAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATGGATGCGGTACAAAAAGCCAACTCTGGTCATCCCGGCGCGCCGATGGGCATGGCTGATATTGCCGAAGTGCTGTGGAACGATTTTCTTA  >  minE/1625905‑1626036
                                                                |                                                                   
tGTCCCTAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATGGATGCGGTACAAAAAGCCAACTCTg                                                                 >  1:1366176/1‑69 (MQ=255)
tGTCCCGAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATGGATGCGGTACAAAAAGCCAActct                                                                  >  1:488779/1‑68 (MQ=255)
tGTCCCGAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATGGATGCGGTACAAAAAGCCAACTCTg                                                                 >  1:2417850/1‑69 (MQ=255)
tGTCCCGAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATGGATGCGGTACAAAAAGCCAACTCTg                                                                 >  1:2273669/1‑69 (MQ=255)
tGTCCCGAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATGGATGCGGTACAAAAAGCCAACTCTg                                                                 >  1:1943670/1‑69 (MQ=255)
  tCCCGAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATGGATGCGGTACAAAAAGCCAACTCTGGt                                                               >  1:2040637/1‑69 (MQ=255)
  tCCCGAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATGGATGCGGTACAAAAAGCCAACTCTGGt                                                               >  1:681678/1‑69 (MQ=255)
    ccGAAAAGACCTTGCCAATGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCa                                                             >  1:2631917/1‑69 (MQ=255)
    ccGAAAAGACCTTGCCAATGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCa                                                             >  1:2534789/1‑69 (MQ=255)
    ccGAAAAGACCTTGCCAATGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCa                                                             >  1:296884/1‑69 (MQ=255)
    ccGAAAAGACCTTGCCAATGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCa                                                             >  1:3048464/1‑69 (MQ=255)
    ccGAAAAGACCTTGCCAATGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCa                                                             >  1:3278930/1‑69 (MQ=255)
    ccGAAAAGACCTTGCCAATGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCa                                                             >  1:2061418/1‑69 (MQ=255)
    ccGAAAAGACCTTGCCAATGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCa                                                             >  1:1951425/1‑69 (MQ=255)
    ccGAAAAGACCTTGCCAATGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCa                                                             >  1:1104030/1‑69 (MQ=255)
    ccGAAAAGACCTTGCCAATGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCa                                                             >  1:1229248/1‑69 (MQ=255)
    ccGAAAAGACCTTGCCAATGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCa                                                             >  1:95675/1‑69 (MQ=255)
    ccGAAAAGACCTTGCCAATGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCa                                                             >  1:1277167/1‑69 (MQ=255)
      gAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATGGATGCGGTACAAAAAGCCAACTCTGGTCAt                                                            <  1:1459215/68‑1 (MQ=255)
      gAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATGGATGCGGTACAAAAAGCCAACTCTGGTCAt                                                            <  1:2804693/68‑1 (MQ=255)
      gAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATGGATGCGGTACAAAAAGCCAACTCTGGTCAt                                                            <  1:1734604/68‑1 (MQ=255)
      gAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATGGATGCGGTACAAAAAGCCAACTCTGGTCAt                                                            <  1:778749/68‑1 (MQ=255)
      gAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATGGATGCGGTACAAAAAGCCAACTCTGGTCAt                                                            <  1:2861694/68‑1 (MQ=255)
      gAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATGGATGCGGTACAAAAAGCCAACTCTGGTCAt                                                            <  1:954214/68‑1 (MQ=255)
       aaaaGACCTTGCCAATGCGATTCGTGCACTCAGTATGTATGCGGTACAAAAAGCCAATTCTGGTCATcc                                                          >  1:648555/1‑69 (MQ=255)
       aaaaGACCTTGCCAATGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATcc                                                          >  1:1415511/1‑69 (MQ=255)
       aaaaGACCTTGCCAATGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATcc                                                          >  1:1982947/1‑69 (MQ=255)
       aaaaGACCTTGCCAATGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATcc                                                          >  1:3296673/1‑69 (MQ=255)
       aaaaGACCTTGCCAATGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATcc                                                          >  1:3046304/1‑69 (MQ=255)
       aaaaGACCTTGCCAATGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATcc                                                          >  1:1087918/1‑69 (MQ=255)
       aaaaGACCTTGCCAATGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATcc                                                          >  1:734957/1‑69 (MQ=255)
       aaaaGACCTTGCCAATGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATcc                                                          >  1:2464373/1‑69 (MQ=255)
       aaaaGACCTTGCCAATGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATcc                                                          >  1:2504303/1‑69 (MQ=255)
       aaaaGACCTTGCCAATGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATcc                                                          >  1:2634592/1‑69 (MQ=255)
       aaaaGACCTTGCCAATGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATcc                                                          >  1:1416057/1‑69 (MQ=255)
         aaGACCTTGCCAATGCGATTCGCGCACTCAGTATGGATGCGGTACAAAAAGCCAACTCTGGTCATCCCg                                                        >  1:1132382/1‑69 (MQ=255)
                tGCCAATGCGATTCGCGCACTCAGTATGGATGCGGTACAAAAAGCCAACTCTGGTCATCCCGGCGCGcc                                                 <  1:2089424/69‑1 (MQ=255)
                tGCCAATGCGATTCGCGCACTCAGTATGGATGCGGTACAAAAAGCCAACTCTGGTCATCCCGGCGCGcc                                                 <  1:415433/69‑1 (MQ=255)
                      tGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATCCCGGCGCGcc                                                 <  1:2192206/63‑1 (MQ=255)
                      tGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATCCCGGCGCGcc                                                 <  1:2224178/63‑1 (MQ=255)
                      tGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATCCCGGCGCGcc                                                 <  1:3159474/63‑1 (MQ=255)
                      tGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATCCCGGCGCGcc                                                 <  1:226248/63‑1 (MQ=255)
                      tGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATCCCGGCGCGcc                                                 <  1:111743/63‑1 (MQ=255)
                      tGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATCCCGGCGCGcc                                                 <  1:913926/63‑1 (MQ=255)
                      tGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATCCCGGCGCGcc                                                 <  1:671899/63‑1 (MQ=255)
                      tGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATCCCGGCGCGcc                                                 <  1:2410662/63‑1 (MQ=255)
                      tGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATCCCGGCGCGcc                                                 <  1:1835294/63‑1 (MQ=255)
                       gCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATCCCGGCGCGcc                                                 <  1:1660726/62‑1 (MQ=255)
                       gCGATTCGCGCACTCAGTATGGATGCGGTACAAAAAGCCAACTCTGGTCATCCCGGCGCGCCGATGGGc                                          >  1:2403086/1‑69 (MQ=255)
                       gCGATTCGCGCACTCAGTATGGATGCGGTACAAAAAGCCAACTCTGGTCATCCCGGCGCGCCGATGGGc                                          >  1:130006/1‑69 (MQ=255)
                          aTTCGCGCACTCAGTATGGATGCGGTACAAAAAGCCAACTCTGGTCATCCCGGCGCGCCGATGGGCATg                                       <  1:2592237/69‑1 (MQ=255)
                          aTTCGCGCACTCAGTATGGATGCGGTACAAAAAGCCAACTCTGGTCATCCCGGCGCGCCGATGGGCATg                                       <  1:1852300/69‑1 (MQ=255)
                                gcACTCAGTATTGATGCGGTACAAAAAGCCAACTCTGGTCATCCCGGCGCGCCGATGGGCATGGCTGa                                  <  1:454252/68‑1 (MQ=255)
                                gcACTCAGTATGTATGCGGTACAAAAAGCCAACTCTGGTCATCCCGGCGCGCCGATGGGCATGGCTGa                                  <  1:1506437/68‑1 (MQ=255)
                                gcACTCAGTATGGATGCGGTACAAAAAGCCAACTCTGGTCATCCCGGCGCGCCGATGGGCATGGCTGa                                  <  1:3199183/68‑1 (MQ=255)
                                gcACTCAGTATGGATGCGGTACAAAAAGCCAACTCTGGTCATCCCGGCGCGCCGATGGGCATGGCTGa                                  <  1:2757015/68‑1 (MQ=255)
                                gcACTCAGTATGGATGCGGTACAAAAAGCCAACTCTGGTCATCCCGGCGCGCCGATGGGCATGGCTGa                                  <  1:657303/68‑1 (MQ=255)
                                  aCTCAGTATGGATGCGGTACAAAAAGCCAACTCTGGTCATCCCGGCGCGCCGATGGGCATGGCTGa                                  <  1:991150/66‑1 (MQ=255)
                                     cAGTATGGATGCGGTACAAAAAGCCAACTCTGGTCATCCCGGCGCGCCGATGGGCATGGCTGa                                  >  1:1020777/1‑63 (MQ=255)
                                     cAGTATGGATGCGGTACAAAAAGCCAACTCTGGTCATCCCGGCGCGCCGATGGGCATGGCTGa                                  >  1:317903/1‑63 (MQ=255)
                                     cAGTATGGATGCGGTACAAAAAGCCAACTCTGGTCATCCCGGCGCGCCGATGGGCATGGCTGa                                  >  1:3086112/1‑63 (MQ=255)
                                      aGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATCCCGGCGCGCCGATGGGCATGGCTGATATTg                             >  1:2713838/1‑67 (MQ=255)
                                      aGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATCCCGGCGCGCCGATGGGCATGGCTGATATTGc                            >  1:2453288/1‑68 (MQ=255)
                                      aGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATCCCGGCGCGCCGATGGGCATGGCTGATATTGc                            >  1:383647/1‑68 (MQ=255)
                                      aGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATCCCGGCGCGCCGATGGGCATGGCTGATATTGc                            >  1:2238516/1‑68 (MQ=255)
                                      aGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATCCCGGCGCGCCGATGGGCATGGCTGATATTGc                            >  1:429270/1‑68 (MQ=255)
                                      aGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATCCCGGCGCGCCGATGGGCATGGCTGATATTGc                            >  1:1587062/1‑68 (MQ=255)
                                      aGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATCCCGGCGCGCCGATGGGCATGGCTGATATTGc                            >  1:2812059/1‑68 (MQ=255)
                                      aGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATCCCGGCGCGCCGATGGGCATGGCTGATATTGc                            >  1:1182585/1‑68 (MQ=255)
                                      aGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATCCCGGCGCGCCGATGGGCATGGCTGATATTGc                            >  1:2738851/1‑68 (MQ=255)
                                        tATGGATGCGGTACAAAAAGCCAACTCTGGTCATCCCGGCGCGCCGATGGGCATGGCTGATATTGCCGa                         >  1:2464715/1‑69 (MQ=255)
                                          tGGATGCGGTACAAAAAGCCAACTCTGGTCATCCCGGCGCGCCGa                                               >  1:2350139/1‑45 (MQ=255)
                                          tGGATGCGGTACAAAAAGCCAACTCTGGTCATCCCGGCGCGCCGATGGGCATGGCTGa                                  <  1:2536156/58‑1 (MQ=255)
                                          tGGATGCGGTACAAAAAGCCAACTCTGGTCATCCCGGCGCGCCGATGGGCATGGCTGa                                  <  1:1598875/58‑1 (MQ=255)
                                          tGGATGCGGTACAAAAAGCCAACTCTGGTCATCCCGGCGCGCCGATGGGCATGGCTGa                                  <  1:1457932/58‑1 (MQ=255)
                                          tGGATGCGGTACAAAAAGCCAACTCTGGTCATCCCGGCGCGCCGATGGGCATGGCTGa                                  >  1:386371/1‑58 (MQ=255)
                                          tGGATGCGGTACAAAAAGCCAACTCTGGTCATCCCGGCGCGCCGATGGGCATGGCTGa                                  <  1:930509/58‑1 (MQ=255)
                                          tGGATGCGGTACAAAAAGCCAACTCTGGTCATCCCGGCGCGCCGATGGGCATGGCTGa                                  <  1:3347919/58‑1 (MQ=255)
                                          tGGATGCGGTACAAAAAGCCAACTCTGGTCATCCCGGCGCGCCGATGGGCATGGCTGa                                  >  1:3139434/1‑58 (MQ=255)
                                          tGGATGCGGTACAAAAAGCCAACTCTGGTCATCCCGGCGCGCCGATGGGCATGGCTGa                                  <  1:2796950/58‑1 (MQ=255)
                                          tGGATGCGGTACAAAAAGCCAACTCTGGTCATCCCGGCGCGCCGATGGGCATGGCTGa                                  <  1:281787/58‑1 (MQ=255)
                                          tGGATGCGGTACAAAAAGCCAACTCTGGTCATCCCGGCGCGCCGATGGGCATGGCTGATATTGCCGAAg                       >  1:2609407/1‑69 (MQ=255)
                                          tGGATGCGGTACAAAAAGCCAACTCTGGTCATCCCGGCGCGCCGATGGGCATGGCTGATATTGCCGAAg                       >  1:2179990/1‑69 (MQ=255)
                                          tGGATGCGGTACAAAAAGCCAACTCTGGTCATCCCGGCGCGCCGATGGGCATGGCTGATATTGCCGAAg                       >  1:2343484/1‑69 (MQ=255)
                                          tGGATGCGGTACAAAAAGCCAACTCTGGTCATCCCGGCGCGCCGATGGGCATGGCTGATATTGCCGAAg                       >  1:479426/1‑69 (MQ=255)
                                           ggATGCGGTACAAAAAGCCAACTCTGGTCATCCCGGCGCGCCGATGGGCATGGCTGa                                  <  1:409518/57‑1 (MQ=255)
                                            gATGCGGTACAAAAAGCCAACTCTGGTCATCCCGGCGCGCCGATGGTCATGGCTGATATTGCCGAAGTg                     >  1:100983/1‑69 (MQ=255)
                                            gATGCGGTACAAAAAGCCAACTCTGGTCATCCCGGCGCGCCGATGGGCATGGCTGATATTGCCGAAGTg                     >  1:2423853/1‑69 (MQ=255)
                                            gATGCGGTACAAAAAGCCAACTCTGGTCATCCCGGCGCGCCGATGGGCATGGCTGATATTGCCGAAGTg                     >  1:266368/1‑69 (MQ=255)
                                            gATGCGGTACAAAAAGCCAACTCTGGTCATCCCGGCGCGCCGATGGGCATGGCTGATATTGCCGAAGTg                     >  1:1554936/1‑69 (MQ=255)
                                            gATGCGGTACAAAAAGCCAACTCTGGTCATCCCGGCGCGCCGATGGGCATGGCTGATATTGCCGAAGTg                     >  1:35794/1‑69 (MQ=255)
                                              tGCGGTACAAAAAGCCAACTCTGGTCATCCCGGCGCGCCGATGGGCATGGCTGa                                  <  1:1765636/54‑1 (MQ=255)
                                              tGCGGTACAAAAAGCCAACTCTGGTCATCCCGGCGCGCCGATGGGCATGGCTGa                                  <  1:1814134/54‑1 (MQ=255)
                                              tGCGGTACAAAAAGCCAACTCTGGTCATCCCGGCGCGCCGATGGGCATGGCTGa                                  <  1:1284804/54‑1 (MQ=255)
                                              tGCGGTACAAAAAGCCAACTCTGGTCATCCCGGCGCGCCGATGGGCATGGCTGa                                  <  1:1231671/54‑1 (MQ=255)
                                              tGCGGTACAAAAAGCCAACTCTGGTCATCCCGGCGCGCCGATGGGCATGGCTGa                                  <  1:190800/54‑1 (MQ=255)
                                              tGCGGTACAAAAAGCCAACTCTGGTCATCCCGGCGCGCCGATGGGCATGGCTGa                                  <  1:209241/54‑1 (MQ=255)
                                                       aaaaGCCAACTCTGGTCATCCCGGCGCGCCGATGGGCATGGCTGATATTGACGAAGTGCTGTGGAACGa          >  1:1041008/1‑69 (MQ=255)
                                                               aCTCTGGTCATCCCGGCGCGCCGATGGGCATGGCTGATATTGCCGAAGTGCTGTGGAACGATTTTCTTa  <  1:1975165/69‑1 (MQ=255)
                                                               aCTCTGGTCATCCCGGCGCACCGATGGGCATGGCTGATATTGCCGAAGTGCTGTGGAACGATTTTCTTa  <  1:2479947/69‑1 (MQ=255)
                                                                |                                                                   
TGTCCCGAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATGGATGCGGTACAAAAAGCCAACTCTGGTCATCCCGGCGCGCCGATGGGCATGGCTGATATTGCCGAAGTGCTGTGGAACGATTTTCTTA  >  minE/1625905‑1626036

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