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 309,067 T→A 40.5% V37V (GTA→GTT)  ybaJ ← hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE309,0670TA40.5% 61.0 / 102.4 106V37V (GTA→GTT) ybaJhypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (43/20);  new base A (22/21);  total (65/41)
Fisher's exact test for biased strand distribution p-value = 1.04e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 117 total aligned reads displayed.

CGCAATATGCTCAATCAGTTCATTCAACTGGAGGTTGATCGCCGAGGTTGGGTCGTTTACCCAGCCATGATTGCTTTCTTCAAGGTTTGCAAGGCAGTCATGATACAGGGTTTCACAGAGAAAC  >  minE/309010‑309133
                                                         |                                                                  
cGCAATATGCTCAATCAGTTCATTCAACTGGAGGTTGATCGCCGAGGTTGGGTCGTTTACCCAGCCATg                                                         <  1:2487173/69‑1 (MQ=255)
cGCAATATGCTCAATCAGTTCATTCAACTGGAGGTTGATCGCCGAGGTTGGGTCGTTTACCCAGCCATg                                                         <  1:2431345/69‑1 (MQ=255)
cGCAATATGCTCAATCAGTTCATTCAACTGGAGGTTGATCGCCGAGGTTGGGTCGTTTACCCAGCCATg                                                         <  1:786310/69‑1 (MQ=255)
cGCAATATGCTCAATCAGTTCATTCAACTGGAGGTTGATCGCCGAGGTTGGGGCGTTTACCCAGCCATg                                                         <  1:2441744/69‑1 (MQ=255)
       tGCTCAATCAGTTCATTCAACTGGAGGTTGATCGCCGAGGTTGGGTCGTTTa                                                                   >  1:1926650/1‑52 (MQ=255)
       tGCTCAATCAGTTCATTCAACTGGAGGTTGATCGCCGAGGTTGGGTCGTTTACCCAGCCATGATTGCtt                                                  >  1:1877714/1‑69 (MQ=255)
       tGCTCAATCAGTTCATTCAACTGGAGGTTGATCGCCGAGGTTGGGTCGTTTACCCAGCCATGATTGCtt                                                  >  1:2769266/1‑69 (MQ=255)
       tGCTCAATCAGTTCATTCAACTGGAGGTTGATCGCCGAGGTTGGGTCGTTTACCCAGCCATGATTGCtt                                                  >  1:2593404/1‑69 (MQ=255)
       tGCTCAATCAGTTCATTCAACTGGAGGTTGATCGCCGAGGTTGGGTCGTTTACCCAGCCATGATTGCtt                                                  >  1:2388379/1‑69 (MQ=255)
       tGCTCAATCAGTTCATTCAACTGGAGGTTGATCGCCGAGGTTGGGTCGTTTACCCAGCCATGATTGCtt                                                  >  1:2369068/1‑69 (MQ=255)
       tGCTCAATCAGTTCATTCAACTGGAGGTTGATCGCCGAGGTTGGGTCGTTTACCCAGCCATGATTGCtt                                                  >  1:2349654/1‑69 (MQ=255)
       tGCTCAATCAGTTCATTCAACTGGAGGTTGATCGCCGAGGTTGGGTCGTTTACCCAGCCATGATTGCtt                                                  >  1:1000449/1‑69 (MQ=255)
       tGCTCAATCAGTTCATTCAACTGGAGGTTGATCGCCGAGGTTGGGTCGTTTACCCAGCCATGATTGCtt                                                  >  1:905138/1‑69 (MQ=255)
       tGCTCAATCAGTTCATTCAACTGGAGGTTGATCGCCGAGGTTGGGTCGTTAAccc                                                                >  1:624067/1‑55 (MQ=255)
       tGCTCAATCAGTTCATTCAACTGGAGGTTGATCGCCGAGGTTGGGTCGTTAACCCAGCCAt                                                          >  1:303110/1‑61 (MQ=255)
       tGCTCAATCAGTTCATTCAACTGGAGGTTGATCGCCGAGGTTGGGTCGTTAACCCAGCCAt                                                          >  1:3266917/1‑61 (MQ=255)
       tGCTCAATCAGTTCATTCAACTGGAGGTTGATCGCCGAGGTTGGGTCGTTAACCCAGCCAt                                                          >  1:3360585/1‑61 (MQ=255)
       tGCTCAATCAGTTCATTCAACTGGAGGTTGATCGCCGAGGTTGGGTCGTTAACCCAGCCAt                                                          >  1:207719/1‑61 (MQ=255)
       tGCTCAATCAGTTCATTCAACTGGAGGTTGATCGCCGAGGTTGGGTCGTTAACCCAGCCAt                                                          >  1:1728578/1‑61 (MQ=255)
       tGCTCAATCAGTTCATTCAACTGGAGGTTGATCGCCGAGGTTGGGTCGTTAACCCAGCCAt                                                          >  1:1607449/1‑61 (MQ=255)
       tGCTCAATCAGTTCATTCAACTGGAGGTTGATCGCCGAGGTTGGGTCGTTAACCCAGCCAt                                                          >  1:2329891/1‑61 (MQ=255)
       tGCTCAATCAGTTCATTCAACTGGAGGTTGATCGCCGAGGTTGGGTCGTTAACCCAGCCAt                                                          >  1:3099993/1‑61 (MQ=255)
       tGCTCAATCAGTTCATTCAACTGGAGGTTGATCGCCGAGGTTGGGTCGTTAACCCAGCCAt                                                          >  1:2430346/1‑61 (MQ=255)
       tGCTCAATCAGTTCATTCAACTGGAGGTTGATCGCCGAGGTTGGGTCGTTAACCCAGCCAt                                                          >  1:2539540/1‑61 (MQ=255)
       tGCTCAATCAGTTCATTCAACTGGAGGTTGATCGCCGAGGTTGGGTCGTTAACCCAGCCAt                                                          >  1:2941244/1‑61 (MQ=255)
       tGCTCAATCAGTTCATTCAACTGGAGGTTGATCGCCGAGGTTGGGTCGTTAACCCAGCCAt                                                          >  1:1082986/1‑61 (MQ=255)
       tGCTCAATCAGTTCATTCAACTGGAGGTTGATCGCCGAGGTTGGGTCGTTAACCCAGCCAt                                                          >  1:1491276/1‑61 (MQ=255)
       tGCTCAATCAGTTCATTCAACTGGAGGTTGATCGCCGAGGTTGGGTCGTTAACCCAGCCAt                                                          >  1:1444708/1‑61 (MQ=255)
       tGCTCAATCAGTTCATTCAACTGGAGGTTGATCGCCGAGGTTGGGTCGTTAACCCAGCCAt                                                          >  1:2738390/1‑61 (MQ=255)
       tGCTCAATCAGTTCATTCAACTGGAGGTTGATCGCCGAGGTTGGGTCGTTAACCCAGCCAt                                                          >  1:662555/1‑61 (MQ=255)
       tGCTCAATCAGTTCATTCAACTGGAGGTTGATCGCCGAGGTTGGGGCGTTTACCCAGCCATGATTGCtt                                                  >  1:2369988/1‑69 (MQ=255)
       tGCTCAATCAGTTCATTAAACTGGAGGTTGATCGCCGAGGTTGGGTCGttt                                                                    >  1:418770/1‑51 (MQ=255)
         cTCAATCAGTTCATTCAACTGGAGGTTGATCGCCGAGGTTGGGTCGTTTAccc                                                                <  1:1386061/53‑1 (MQ=255)
         cTCAATCAGTTCATTCAACTGGAGGTTGATCGCCGAGGTTGGGTCGTTTAccc                                                                <  1:2930028/53‑1 (MQ=255)
         cTCAATCAGTTCATTCAACTGGAGGTTGATCGCCGAGGTTGGGTCGTTTAccc                                                                <  1:1334782/53‑1 (MQ=255)
         cTCAATCAGTTCATTCAACTGGAGGTTGATCGCCGAGGTTGGGTCGTTTAccc                                                                <  1:1539035/53‑1 (MQ=255)
         cTCAATCAGTTCATTCAACTGGAGGTTGATCGCCGAGGTTGGGTCGTTTAccc                                                                <  1:1588289/53‑1 (MQ=255)
                aGTTCATTCAACTGGAGGTTGATCGCCGAGGTTGGGTCGTTTACCCAGCCATGATTGCTTTCTTCAAgg                                         >  1:1423775/1‑69 (MQ=255)
                aGTTCATTCAACTGGAGGTTGATCGCCGAGGTTGGGTCGTTTACCCAGCCATGATTGCTTTCTTCAAgg                                         >  1:523560/1‑69 (MQ=255)
                aGTTCATTCAACTGGAGGTTGATCGCCGAGGTTGGGTCGTTTACCCAGCCATGATTGCTTTCTTCAAgg                                         >  1:2483771/1‑69 (MQ=255)
                  ttcattcaACTGGAGGTTGATCGCCGAGGTTGGGTCGTTAACCCAGCCATGATTGCTTTCTTCAAGGt                                        <  1:2018233/68‑1 (MQ=255)
                  ttcattcaACTGGAGGTTGATCGCCGAGGTTGGGTCGTTAACCCAGCCATGATTGCTTTCTTCAAGGt                                        <  1:1547397/68‑1 (MQ=255)
                  ttcattcaACTGGAGGTTGATCGCCGAGGTTGGGTCGTTAACCCAGCCATGATTGCTTTCTTCAAGGt                                        <  1:2527401/68‑1 (MQ=255)
                  ttcattcaACTGGAGGTTGATCGCCGAGGTTGGGTCGTTAACCCAGCCATGATTGCTTTCTTCAAGGt                                        <  1:2486947/68‑1 (MQ=255)
                  ttcattcaACTGGAGGTTGATCGCCGAGGTTGGGTCGTTAACCCAGCCATGATTGCTTTCTTCAAGGt                                        <  1:2437302/68‑1 (MQ=255)
                  ttcattcaACTGGAGGTTGATCGCCGAGGTTGGGTCGTTAACCCAGCCATGATTGCTTTCTTCAAGGt                                        <  1:1165933/68‑1 (MQ=255)
                  ttcattcaACTGGAGGTTGATCGCCGAGGTTGGGTCGTTAACCCAGCCATGATTGCTTTCTTCAAGGt                                        <  1:1547453/68‑1 (MQ=255)
                  ttcattcaACTGGAGGTTGATCGCCGAGGTTGGGTCGTTAACCCAGCCATGATTGCTTTCTTCAAGGt                                        <  1:242285/68‑1 (MQ=255)
                  ttcattcaACTGGAGGTTGATCGCCGAGGTTGGGTCGTTAACCCAGCCATGATTGCTTTCTTCAAGGt                                        <  1:497972/68‑1 (MQ=255)
                  ttcattcaACTGGAGGTTGATCGCCGAGGTTGGGTCGTTAACCCAGCCATGATTGCTTTCTTCAAGGt                                        <  1:2143003/68‑1 (MQ=255)
                  ttcattcaACTGGAGGTTGATCGCCGAGGTTGGGTCGTTAACCCAGCCATGATTGCTTTCTTCAAGGt                                        <  1:1584012/68‑1 (MQ=255)
                  ttcattcaACTGGAGGTTGATCGCCGAGGTTGGGTCGTTAACCCAGCCATGATTGCTTTCTTCAAGGt                                        <  1:1313909/68‑1 (MQ=255)
                  ttcattcaACTGGAGGTTGATCGCCGAGGTTGGGTCGTTAACCCAGCCATGATTGCTTTCTTCAAGGt                                        <  1:2391314/68‑1 (MQ=255)
                  ttcattcaACTGGAGGTTGATCGCCGAGGTTGGGGCGTTAACCCAGCCATGATTGCTTTCTTCAAGGt                                        <  1:79358/68‑1 (MQ=255)
                  ttcattcaACTGGAGGTTGATCGCAGAGGTTGGGTCGTTAACCCAGCCATGATTGCTTTCTTCAAGGt                                        <  1:572746/68‑1 (MQ=255)
                   tcattcaACTGGAGGTTGATCGCCGAGGTTGGGTCGTTAACCCAGCCATGATTGCTTTCTTCAAGGt                                        <  1:1518746/67‑1 (MQ=255)
                      ttcaACTGGAGGTTGATCGCCGAGGTTGGGTCGTTTACCCAGCCATGATTGCTTTCTTCAAGGTTTGc                                    <  1:926497/68‑1 (MQ=255)
                      ttcaACTGGAGGTTGATCGCCGAGGTTGGGTCGTTTACCCAGCCATGATTGCTTTCTTCAAGGTTTGc                                    <  1:1582902/68‑1 (MQ=255)
                      ttcaACTGGAGGTTGATCGCCGAGGTTGGGTCGTTTACCCAGCCATGATTGCTTTCTTCAAGGTTTGc                                    <  1:1089756/68‑1 (MQ=255)
                      ttcaACTGGAGGTTGATCGCCGAGGTTGGGTCGTTTACCCAGCCATGATTGCTTTCTTCAAGGTTTGc                                    <  1:2521427/68‑1 (MQ=255)
                      ttcaACTGGAGGTTGATCGCCGAGGTTGGGTCGTTTACCCAGCCATGATTGCTTTCTTCAAGGTTTGc                                    <  1:1572599/68‑1 (MQ=255)
                      ttcaACTGGAGGTTGATCGCCGAGGTTGGGTCGTTTACCCAGCCATGATTGCTTTCTTCAAGGTTTGc                                    <  1:2248999/68‑1 (MQ=255)
                      ttcaACTGGAGGTTGATCGCCGAGGTTGGGTCGTTTACCCAGCCATGATTGCTTTCTTCAAGGTTTGc                                    <  1:418209/68‑1 (MQ=255)
                      ttcaACTGGAGGTTGATCGCCGAGGTTGGGTCGTTTACCCAGCCATGATTGCTTTCTTCAAGGTTTGc                                    <  1:2607730/68‑1 (MQ=255)
                      ttcaACTGGAGGTTGATCGCCGAGGTTGGGTCGTTTACCCAGCCATGATTGCTTTCTTCAAGGTTTGc                                    <  1:2843017/68‑1 (MQ=255)
                        caACTGGAGGTTGATCGCCGAGGTTGGGTCGTTTACCCAGCCATGATTGCTTTCTTCAAGGTTTGCaa                                  >  1:2610202/1‑68 (MQ=255)
                                ggTTGATCGCCGAGGTTGGGTCGTTTACCCAGCCATGATTGCTTTCTTCAAGGTTTGCAAGGCAGTCAt                         <  1:934192/69‑1 (MQ=255)
                                ggTTGATCGCCGAGGTTGGGTCGTTTACCCAGCCATGATTGCTTTCTTCAAGGTTTGCAAGGCAGTCAt                         <  1:1361067/69‑1 (MQ=255)
                                   tGATCGCCGAGGTTGGGTCGTTTACCCAGCCATGATTGCTTTCTTCAAGGTTTGCAAGGCAGTCATGa                       >  1:1418049/1‑68 (MQ=255)
                                   tGATCGCCGAGGTTGGGTCGTTTACCCAGCCATGATTGCTTTCTTCAAGGTTTGCAAGGCAGTCATGa                       >  1:1610190/1‑68 (MQ=255)
                                   tGATCGCCGAGGTTGGGTCGTTTACCCAGCCATGATTGCTTTCTTCAAGGTTTGCAAGGCAGTCATGa                       >  1:872526/1‑68 (MQ=255)
                                   tGATCGCCGAGGTTGGGTCGTTTACCCAGCCATGATTGCTTTCTTCAAGGTTTGCAAGGCAGTCATGa                       >  1:2865968/1‑68 (MQ=255)
                                   tGATAGCCGAGGTTGGGTCGTTTACCCAGCCATGATTGCTTTCTTCAAGGTTTGCAAGGCAGTCATGa                       >  1:2967969/1‑68 (MQ=255)
                                              gTTGGGTCGTTTACCCAGCCATGATTGCTTTCTTCAAGGTTTGCAAGGCAGTCATGATACAGGGttt             >  1:238947/1‑67 (MQ=255)
                                              gTTGGGTCGTTTACCCAGCCATGATTGCTTTCTTCAAGGTTTGCAAGGCAGTCATGATACAGGGttt             >  1:3115398/1‑67 (MQ=255)
                                              gTTGGGTCGTTTACCCAGCCATGATTGCTTTCTTCAAGGTTTGCAAGGCAGTCATGATACAGGGttt             >  1:1839559/1‑67 (MQ=255)
                                                 gggTCGTTTACCCAGCCATGATTGCTTTCTTCAAGGTTTGCAAGGCAGTCATGATACAGGGTTTca           >  1:662229/1‑66 (MQ=255)
                                                 gggTCGTTTACCCAGCCATGATTGCTTTCTTCAAGGTTTGCAAGGCAGTCATGATACAGGGTTTca           >  1:1881262/1‑66 (MQ=255)
                                                 gggTCGTTTACCCAGCCATGATTGCTTTCTTCAAGGTTTGCAAGGCAGTCATGATACAGGGTTTca           >  1:1412857/1‑66 (MQ=255)
                                                 gggTCGTTTACCCAGCCATGATTGCTTTCTTCAAGGTTTGCAAGGCAGTCATGATACAGGGTTTca           >  1:92363/1‑66 (MQ=255)
                                                 gggTCGTTTACCCAGCCATGATTGCTTTCTTCAAGGTTTGCAAGGCAGTCATGATACAGGGTTTca           >  1:1554553/1‑66 (MQ=255)
                                                 gggTCGTTTACCCAGCCATGATTGATTTCTTCAAGGTTTGCAAGGCAGTCATGATACAGGGTTTca           >  1:364639/1‑66 (MQ=255)
                                                    tCGTTTACCCAGCCATGATTGCTTTCTTCAAGGTTTGCAAGGCAGTCATGATACAGGGTTTCACagag      >  1:2885676/1‑68 (MQ=255)
                                                    tCGTTTACCCAGCCATGATTGCTTTCTTCAAGGTTTGCAAGGCAGTCATGATACAGGGTTTCACAgaga     >  1:825030/1‑69 (MQ=255)
                                                    tCGTTTACCCAGCCATGATTGCTTTCTTCAAGGTTTGCAAGGCAGTCATGATACAGGGTTTCACAgaga     >  1:1302769/1‑69 (MQ=255)
                                                    tCGTTTACCCAGCCATGATTGCTTTCTTCAAGGTTTGCAAGGCAGTCATGATACAGGGTTTCACAgaga     >  1:1210376/1‑69 (MQ=255)
                                                    tCGTTTACCCAGCCATGATTGCTTTCTTCAAGGTTTGCAAGGCAGTCATGATACAGGGTTTCACAgaga     >  1:101793/1‑69 (MQ=255)
                                                    tCGTTTACCCAGCCATGATTGCTTTCTTCAAGGTTTGCAAGGCAGTCATGATACAGGGTTTCACAgaga     >  1:1431497/1‑69 (MQ=255)
                                                    tCGTTTACCCAGCCATGATTGCTTTCTTCAAGGTTTGCAAGGCAGTCATGATACAGGGTTTCACAgaga     >  1:1860894/1‑69 (MQ=255)
                                                    tCGTTTACCCAGCCATGATTGCTTTCTTCAAGGTTTGCAAGGCAGTCATGATACAGGGTTTCACAgaga     >  1:3235334/1‑69 (MQ=255)
                                                         tACCCAGCCATGATTGCTTTCTTCAAGGTTTGCAAGGCAGTCATGATACAGGGTTTCACAGAGAAAc  >  1:2332777/1‑67 (MQ=255)
                                                         tACCCAGCCATGATTGCTTTCTTCAAGGTTTGCAAGGCAGTCATGATACAGGGTTTCACAGAGAAAc  >  1:781012/1‑67 (MQ=255)
                                                         tACCCAGCCATGATTGCTTTCTTCAAGGTTTGCAAGGCAGTCATGATACAGGGTTTCACAGAGAAAc  >  1:2972708/1‑67 (MQ=255)
                                                         tACCCAGCCATGATTGCTTTCTTCAAGGTTTGCAAGGCAGTCATGATACAGGGTTTCACAGAGAAAc  >  1:1261306/1‑67 (MQ=255)
                                                         tACCCAGCCATGATTGCTTTCTTCAAGGTTTGCAAGGCAGTCATGATACAGGGTTTCACAGAGAAAc  >  1:257860/1‑67 (MQ=255)
                                                         tACCCAGCCATGATTGCTTTCTTCAAGGTTTGCAAGGCAGTCATGATACAGGGTTTCACAGAGAAAc  >  1:2606361/1‑67 (MQ=255)
                                                         tACCCAGCCATGATTGCTTTCTTCAAGGTTTGCAAGGCAGTCATGATACAGGGTTTCACAGAGAAAc  >  1:2862834/1‑67 (MQ=255)
                                                         tACCCAGCCATGATTGCTTTCTTCAAGGTTTGCAAGGCAGTCATGATACAGGGTTTCACAGAGAAAc  >  1:2643657/1‑67 (MQ=255)
                                                         tACCCAGCCATGATTGCTTTCTTCAAGGTTTGCAAGGCAGTCATGATACAGGGTTTCACAGAGAAAc  >  1:1143063/1‑67 (MQ=255)
                                                         tACCCAGCCATGATTGCTTTCTTCAAGGTTTGCAAGGCAGTCATGATACAGGGTTTCACAGAGAAAc  >  1:2804574/1‑67 (MQ=255)
                                                         |                                                                  
CGCAATATGCTCAATCAGTTCATTCAACTGGAGGTTGATCGCCGAGGTTGGGTCGTTTACCCAGCCATGATTGCTTTCTTCAAGGTTTGCAAGGCAGTCATGATACAGGGTTTCACAGAGAAAC  >  minE/309010‑309133

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