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 1,053,423 G→A 44.1% R63R (CGC→CGT)  ydhL ← conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,053,4230GA44.1% 30.5 / 89.1 114R63R (CGC→CGT) ydhLconserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (12/51);  new base A (40/10);  total (53/61)
Fisher's exact test for biased strand distribution p-value = 8.43e-11
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.68e-01

Only 100 of 129 total aligned reads displayed.

TACGCAAGATTAGGTTCAAAAGAGTGATGGTTGCTCCGGTTCGTCTGATGACGCTGGCTTATTTGCGCGTAATTTGCGCATTAATCGCTGCCGACAAAGGCGCAGCACCTCTTGTTTTTCGCCATCGCTCATTT  >  minE/1053357‑1053490
                                                                  |                                                                   
taCGCAAGATTAGGTTCAAAAGAGTGATGGTTGCTCCGGTTCGTCTGATGACGCTGGCTTATTTgcgc                                                                    >  1:154202/1‑68 (MQ=255)
taCGCAAGATTAGGTTCAAAAGAGTGATGGTTGCTCCGGTTCGTCTGATGACGCTGGCTTATTTgcgc                                                                    >  1:2917271/1‑68 (MQ=255)
taCGCAAGATTAGGTTCAAAAGAGTGATGGTTGCTCCGGTTCGTCTGATGACGCTGGCTTATTTgcgc                                                                    >  1:980225/1‑68 (MQ=255)
taCGCAAGATTAGGTTCAAAAGAGTGATGGTTGCTCCGGTTCGTCTGATGACGCTGGCTTATTTgcgc                                                                    >  1:3213382/1‑68 (MQ=255)
taCGCAAGATTAGGTTCAAAAGAGTGATGGTTGCTCCGGTTCGTCTGATGACGCTGGCTTATTTgcgc                                                                    >  1:2272633/1‑68 (MQ=255)
taCGCAAGATTAGGTTCAAAAGAGTGATGGTTGCTCCGGTTCGTCTGATGACGCTGGCTTATTTgcgc                                                                    >  1:1093540/1‑68 (MQ=255)
taCGCAAGATTAGGTTCAAAAGAGTGATGGTTGCTCCGGTTCGTCTGATGACGCTGGCTTATTTgcgc                                                                    >  1:1946984/1‑68 (MQ=255)
taCGCAAGATTAGGTTCAAAAGAGTGATGGTTGCTCCGGTTCGTCTGATGACGCTGGCTTATTTgcgc                                                                    >  1:2371047/1‑68 (MQ=255)
taCGCAAGATTAGGTTCAAAAGAGTGATGGTTGCTCCGGTTCGTCTGATGACGCTGGCTTATTTgcg                                                                     >  1:2747607/1‑67 (MQ=255)
       gATTAGGTTCAAAAGAGTGATGGTTGCTCCGGTTCGTCTGATGACGCTGGCTTATTTGCGCGTAATTTg                                                            <  1:2348615/69‑1 (MQ=255)
       gATTAGGTTCAAAAGAGTGATGGTTGCTCCGGTTCGTCTGATGACGCTGGCTTATTTGCGCGTAATTTg                                                            <  1:3054830/69‑1 (MQ=255)
         ttAGGTTCAAAAGAGTGATGGTTGCTCCTGTTCGTCTGATGACGCTGGCTTATTTGCGCGTAAttt                                                             >  1:652697/1‑66 (MQ=255)
         ttAGGTTCAAAAGAGTGATGGTTGCTCCGGTTCGTCTGATGACGCTGGCTTATTTGCGCGTAATTTgcg                                                          >  1:2339097/1‑69 (MQ=255)
         ttAGGTTCAAAAGAGTGATGGTTGCTCCGGTTCGTCTGATGACGCTGGCTTATTTGCGCGTAATTTgcg                                                          >  1:1926151/1‑69 (MQ=255)
              ttCAAAAGAGTGATGGTTGCTCCGGTTCGTCTGATGACGCTGGCTTATTTGCGCGTAATTTGCGCAtt                                                      <  1:2243230/68‑1 (MQ=255)
              ttCAAAAGAGTGATGGTTGCTCCGGTTCGTCTGATGACGCTGGCTTATTTGCGCGTAATTTGCGCAtt                                                      <  1:2851950/68‑1 (MQ=255)
              ttCAAAAGAGTGATGGTTGCTCCGGTTCGTCTGATGACGCTGGCTTATTTGCGCGTAATTTGCGCATTa                                                     <  1:1883397/69‑1 (MQ=255)
              ttCAAAAGAGTGATGGTTGCTCCGGTTCGTCTGATGACGCTGGCTTATTTGCGCGTAATTTGCGCATTa                                                     <  1:2494505/69‑1 (MQ=255)
              ttCAAAAGAGTGATGGTTGCTCCGGTTCGTCTGATGACGCTGGCTTATTTGCGCGTAATTTGCGCATTa                                                     <  1:2659437/69‑1 (MQ=255)
              ttCAAAAGAGTGATGGTTGCTCCGGTTCGTCTGATGACGCTGGCTTATTTGCGCGTAATTTGCGCATTa                                                     <  1:2212034/69‑1 (MQ=255)
              ttCAAAAGAGTGATGGTTGCTCCGGTTCGTCTGATGACGCTGGCTTATTTGCGCGTAATTTGCGCATTa                                                     <  1:983165/69‑1 (MQ=255)
              ttCAAAAGAGTGATGGTTGCTCCGGTTCGTCTGATGACGCTGGCTTATTTGCGCGTAATTTGCGCATTa                                                     <  1:2843479/69‑1 (MQ=255)
              ttCAAAAGAGTGATGGTTGCTCCGGTTCGTCTGATGACGCTGGCTTATTTGCGCGTAATTTGCGCATTa                                                     <  1:3223048/69‑1 (MQ=255)
              ttCAAAAGAGTGATGGTTGCTCCGGTTCGTCTGATGACGCTGGCTTATTTGCGCGTAATTTGCGCATTa                                                     <  1:468465/69‑1 (MQ=255)
                  aaaGAGTGATGGTTGCTCCGGTTCGTCTGATGGCGCTGGCTTATTTACTCGTaa                                                                >  1:1694717/1‑54 (MQ=38)
                  aaaGAGTGATGGTTGCTCCGGTTCGTCTGATGGCGCTGGCTTATTTACACGTaa                                                                >  1:1524646/1‑54 (MQ=38)
                  aaaGAGTGATGGTTGCTCCGGTTCGTCTGATGGCGCTGGCTTATTTACACGTAATTTGCGCATTAATc                                                  >  1:1223560/1‑68 (MQ=255)
                  aaaGAGTGATGGTTGCTCCGGTTCGTCTGATGGCGCTGGCTTATTTACACGTAATTTGCGCATTAATc                                                  >  1:1032550/1‑68 (MQ=255)
                  aaaGAGTGATGGTTGCTCCGGTTCGTCTGATGGCGCTGGCTTATTTACACGTAATTTGCGCATTAATCg                                                 >  1:2632797/1‑69 (MQ=255)
                  aaaGAGTGATGGTTGCTCCGGTTCGTCTGATGGCGCTGGCTTATTTACACGTAATTTGCGCATTAATCg                                                 >  1:2582871/1‑69 (MQ=255)
                  aaaGAGTGATGGTTGCTCCGGTTCGTCTGATGGCGCTGGCTTATTTACACGTAATTTGCGCATTAATCg                                                 >  1:2415020/1‑69 (MQ=255)
                  aaaGAGTGATGGTTGCTCCGGTTCGTCTGATGGCGCTGGCTTATTTACACGTAATTTGCGCATTAATCg                                                 >  1:2395309/1‑69 (MQ=255)
                  aaaGAGTGATGGTTGCTCCGGTTCGTCTGATGGCGCTGGCTTATTTACACGTAATTTGCGCATTAATCg                                                 >  1:3128166/1‑69 (MQ=255)
                  aaaGAGTGATGGTTGCTCCGGTTCGTCTGATGGCGCTGGCTTATTTACACGTAATTTGCGCATTAATCg                                                 >  1:3307834/1‑69 (MQ=255)
                  aaaGAGTGATGGTTGCTCCGGTTCGTCTGATGGCGCTGGCTTATTTACACGTAATTTGCGCATTAATCg                                                 >  1:47590/1‑69 (MQ=255)
                  aaaGAGTGATGGTTGCTCCGGTTCGTCTGATGGCGCTGGCTTATTTACACGTAATTTGCGCATTAATCg                                                 >  1:631531/1‑69 (MQ=255)
                  aaaGAGTGATGGTTGCTCCGGTTCGTCTGATGGCGCTGGCTTATTTACACGTAATTTGCGCATTAATCg                                                 >  1:2451220/1‑69 (MQ=255)
                  aaaGAGTGATGGTTGCTCCGGTTCGTCTGATGGCGCTGGCTTATTTACACGTAATTTGCGCATTAATCg                                                 >  1:1629448/1‑69 (MQ=255)
                  aaaGAGTGATGGTTGCTCCGGTTCGTCTGATGGCGCTGGCTTATTTACACGTAATTTGCGCATTAATCg                                                 >  1:2173437/1‑69 (MQ=255)
                  aaaGAGTGATGGTTGCTCCGGTTCGTCTGATGGCGCTGGCTTATTTACACGTAATTTGCGCATTAATCg                                                 >  1:205894/1‑69 (MQ=255)
                  aaaGAGTGATGGTTGCTCCGGTTCGTCTGATGGCGCTGGCTTATTTACACGTAATTTGCGCATTAATCg                                                 >  1:1803228/1‑69 (MQ=255)
                  aaaGAGTGATGGTTGCTCCGGTTCGTCTGATGGCGCTGGCTTATTTACACGTAATTTGCGCATTAATCg                                                 >  1:1694820/1‑69 (MQ=255)
                  aaaGAGTGATGGTTGCTCCGGTTCGTCTGATGGCGCTGGCTTATTTACACGTAATTTGCGCATTAATCg                                                 >  1:1174487/1‑69 (MQ=255)
                  aaaGAGTGATGGTTGCTCCGGTTCGTCTGATGGCGCTGGCTTATTTACACGTAATTTGCGCATTAATCg                                                 >  1:1083129/1‑69 (MQ=255)
                  aaaGAGTGATGGTTGCTCCGGTTCGTCTGATGGCGCTGGCTTATTTACACGTAATTTGCGCATTAATCg                                                 >  1:1119663/1‑69 (MQ=255)
                  aaaGAGTGATGGTTGCTCCGGTTCGTCTGATGACTCTGGCTTATTTGCGCGTAATTTGCGCATTAATc                                                  <  1:894442/68‑1 (MQ=255)
                  aaaGAGTGATGGTTGCTCCGGTTCGTCTGATGACGCTGGCTTATTTGCGCGTAATTTGCGCATTAATc                                                  <  1:1652598/68‑1 (MQ=255)
                  aaaGAGTGATGGTTGCTCCGGTTCGTCTGATGACGCTGGCTTATTTGCGCGTAATTTGCGCATTAATc                                                  <  1:3288903/68‑1 (MQ=255)
                  aaaGAGTGATGGTTGCTCCGGTTCGTCTGATGACGCTGGCTTATTTGCGCGTAATTTGCGCATTAATc                                                  <  1:936708/68‑1 (MQ=255)
                  aaaGAGTGATGGTTGCTCCGGTTCGTCTGATGACGCTGGCTTATTTGCGCGTAATTTGCGCATTAATc                                                  <  1:3361129/68‑1 (MQ=255)
                  aaaGAGTGAT‑GTTGCTCCGGTTCGTCTGATGGCGCTGGCTTATTTACACGTAATTTGCGCATTAATCGc                                                >  1:3394372/1‑69 (MQ=255)
                   aaGAGTGATGGTTGCTCCGGTTCGTCTGATGACGCTGGCTTATTTGCGCGTAATTTGCGCATTAATc                                                  <  1:2434502/67‑1 (MQ=255)
                            ggTTGCTCCGGTTCGTCTGATGGCGCTGGCTTATTTACACGTAATTTgcgc                                                         >  1:2188047/1‑51 (MQ=38)
                            ggTTGCTCCGGTTCGTCTGATGGCGCTGGCTTATTTACACGTAATTTgcgc                                                         >  1:1442556/1‑51 (MQ=38)
                            ggTTGCTCCGGTTCGTCTGATGGCGCTGGCTTATTTACACGTAATTTgcgc                                                         >  1:114311/1‑51 (MQ=38)
                            ggTTGCTCCGGTTCGTCTGATGGCGCTGGCTTATTTACACGTAATTTgcgc                                                         >  1:1237320/1‑51 (MQ=38)
                            ggTTGCTCCGGTTCGTCTGATGGCGCTGGCTTATTTACACGTAATTTgcgc                                                         >  1:318504/1‑51 (MQ=38)
                            ggTTGCTCCGGTTCGTCTGATGGCGCTGGCTTATTTACACGTAATTTgcgc                                                         >  1:3286518/1‑51 (MQ=38)
                            ggTTGCTCCGGTTCGTCTGATGGCGCTGGCTTATTTACACGTAATTTgcgc                                                         >  1:2670275/1‑51 (MQ=38)
                            ggTTGCTCCGGTTCGTCTGATGGCGCTGGCTTATTTACACGTAATTTgcgc                                                         >  1:668064/1‑51 (MQ=38)
                            ggTTGCTCCGGTTCGTCTGATGGCGCTGGCTTATTTACACGTAATTTgcgc                                                         >  1:847871/1‑51 (MQ=38)
                            ggTTGCTCCGGTTCGTCTGATGGCGCTGGCTTATTTACACGTAATTTgcgc                                                         >  1:2259900/1‑51 (MQ=38)
                            ggTTGCTCCGGTTCGTCTGATGGCGCTGGCTTATTTACACGTAATTTgcgc                                                         >  1:1023237/1‑51 (MQ=38)
                             gTTGCTCCGGTTCGTCTGATGACGCTGGCTTATTTGCGCGTAATTTGCGCATTAATCGCTGCCGACaaa                                      >  1:154982/1‑69 (MQ=255)
                             gTTGCTCCGGTTCGTCTGATGACGCTGGCTTATTTGCGCGTAATTTGCGCATTAATCGCTGCCGACaaa                                      >  1:2479902/1‑69 (MQ=255)
                             gTTGCTCCGGTTCGTCTGATGACGCTGGCTTATTTGCGCGTAATTTGCGCATTAATCGCTGCCGACaaa                                      >  1:2982767/1‑69 (MQ=255)
                             gTTGCTCCGGTTCGTCTGATGACGCTGGCTTATTTGCGCGTAATTTGCGCATTAATCGCTGCCGACaaa                                      >  1:3120140/1‑69 (MQ=255)
                             gTTGCTCCGGTTCGTCTGATGACGCTGGCTTATTTGCGCGTAATTTGCGCATTAATCGCTGCCGACaaa                                      >  1:2246531/1‑69 (MQ=255)
                             gTTGCTCCGGTTCGTCTGATGACGCTGGCTTATTTGCGCGTAATTTGCGCATTAATCGCTGCCGACaa                                       >  1:1308642/1‑68 (MQ=255)
                               tGCTCCGGTTCGTCTGATGACGCTGGCTTATTTGCGCGTAATTTGCGCATTAATCGCTGCCGACAAAgg                                    <  1:105585/69‑1 (MQ=255)
                               tGCTCCGGTTCGTCTGATGACGCTGGCTTATTTGCGCGTAATTTGCGCATTAATCGCTGCCGACAAAgg                                    <  1:3026458/69‑1 (MQ=255)
                               tGCTCCGGTTCGTCTGATGACGCTGGCTTATTTGCGCGTAATTTGCGCATTAATCGCTGCCGACAAAgg                                    <  1:724330/69‑1 (MQ=255)
                                   ccGGTTCGTCTGATGGCGCTGGCTTATTTACACGTAATTTGCGCATTAATCGCTGCCGACAAAGgcgc                                 <  1:415311/68‑1 (MQ=255)
                                   ccGGTTCGTCTGATGGCGCTGGCTTATTTACACGTAATTTGCGCATTAATCGCTGCCGACAAAGgcgc                                 <  1:3074220/68‑1 (MQ=255)
                                   ccGGTTCGTCTGATGGCGCTGGCTTATTTACACGTAATTTGCGCATTAATCGCTGCCGACAAAGgcgc                                 <  1:2452363/68‑1 (MQ=255)
                                   ccGGTTCGTCTGATGGCGCTGGCTTATTTACACGTAATTTGCGCATTAATCGCTGCCGACAAAGgcgc                                 <  1:2187714/68‑1 (MQ=255)
                                   ccGGTTCGTCTGATGGCGCTGGCTTATTTACACGTAATTTGCGCATTAATCGCTGCCGACAAAGgcgc                                 <  1:2318761/68‑1 (MQ=255)
                                   ccGGTTCGTCTGATGGCGCTGGCTTATTTACACGTAATTTGCGCATTAATCGCTGCCGACAAAGgcgc                                 <  1:1013384/68‑1 (MQ=255)
                                   ccGGTTCGTCTGATGGCGCTGGCTTATTTACACGTAATTTGCGCATTAATCGCTGCCGACAAAGgcgc                                 <  1:1754555/68‑1 (MQ=255)
                                   ccGGTTCGTCTGATGGCGCTGGCTTATTTACACGTAATTTGCGCATTAATCGCTGCCGACAAAGgcgc                                 <  1:1448926/68‑1 (MQ=255)
                                   ccGGTTCGTCTGATGACGCTGGCTTATTTGCGCGTAATTTGCGCATTAATCGCTGCCGACAAAGgcgc                                 >  1:2724535/1‑68 (MQ=255)
                                      gTTCGTCTGATGACGCTGGCTTATTTGCGCGTAATTTGCGCATTAATCGCTGCCGACAACGGCgcagc                              <  1:754322/68‑1 (MQ=255)
                                      gTTCGTCTGATGACGCTGGCTTATTTGCGCGTAATTTGCGCATTAATCGCTGCCGACAAAGGCgcagc                              <  1:422176/68‑1 (MQ=255)
                                      gTTCGTCTGATGACGCTGGCTTATTTGCGCGTAATTTGCGCATTAATCGCTGCCGACAAAGGCgcagc                              <  1:2100917/68‑1 (MQ=255)
                                      gTTCGTCTGATGACGCTGGCTTATTTGCGCGTAATTTGCGCATTAATCGCTGCCGACAAAGGCgcagc                              <  1:1984322/68‑1 (MQ=255)
                                              gatgaCGCTGGCTTATTTGCGCGTAATTTGCGCATTa                                                     <  1:3339052/37‑1 (MQ=255)
                                                    gCTGGCTTATTTGCGCGTAATTTGCGCATTAATCGCTGCCGACAAAGGCGCAGCACCTCTTGTTTTTCg               <  1:1040522/69‑1 (MQ=255)
                                                    gCTGGCTTATTTGCGCGTAATTTGCGCATTAATCGCTGCCGACAAAGGCGCAGCACCTCTTGTTTTTCg               <  1:317329/69‑1 (MQ=255)
                                                     cTGGCTTATTTGCGCGTAATTTGCGCATTAATCGCTGCCGACAAAGGCGCAGCACCTCTTGTTTTTCg               <  1:1377060/68‑1 (MQ=255)
                                                         cTTATTTGCGCGTATTTTGCGCATTAATCGCTGACGACAAAGGCgcagc                              <  1:2583782/49‑1 (MQ=255)
                                                               tGCGCGTAATTTGCGCATTAATCGCTGCCGACAAAGGCGCAGCACCTCTTGTTTTTCGCCATCGCTCa     <  1:2400779/68‑1 (MQ=255)
                                                               tGCGCGTAATTTGCGCATTAATCGCTGCCGACAAAGGCGCAGCACCTCTTGTTTTTCGCCATCGCTCa     <  1:1206270/68‑1 (MQ=255)
                                                               tGCGCGTAATTTGCGCATTAATCGCTGCCGACAAAGGCGCAGCACCTCTTGTTTTTCGCCATCGCTCa     <  1:1228086/68‑1 (MQ=255)
                                                               tGCGCGTAATTTGCGCATTAATCGCTGCCGACAAAGGCGCAGCACCTCTTGTTTTTCGCCATCGCTCa     <  1:880338/68‑1 (MQ=255)
                                                               tGCGCGTAATTTGCGCATTAATCGCTGCCGACAAAGGCGCAGCACCTCTTGTTTTTCGCCATCGCTCa     <  1:825515/68‑1 (MQ=255)
                                                               tGCGCGTAATTTGCGCATTAATCGCTGCCGACAAAGGCGCAGCACCTCTTGTTTTTCGCCATCGCTCa     <  1:3216741/68‑1 (MQ=255)
                                                               tGCGCGTAATTTGCGCATTAATCGCTGCCGACAAAGGCGCAGCACCTCTTGTTTTTCGCCATCGCTCa     <  1:2979983/68‑1 (MQ=255)
                                                               tGCGCGTAATTTGCGCATTAATCGCTGCCGACAAAGGCGCAGCACCTCTTGTTTTTCGCCATCGCTCa     <  1:3371500/68‑1 (MQ=255)
                                                                  gcgTAATTTGCGCATTAATCGCTGCCGACAAAGGCGCAGCACCTCTTGTTTTTCGCCATCGCTCAttt  <  1:1756424/68‑1 (MQ=255)
                                                                  gcgTAATTTGCGCATTAATCGCTGCCGACAAAGGCGCAGCACCTCTTGTTTTTCGCCATCGCTCAttt  <  1:9196/68‑1 (MQ=255)
                                                                  |                                                                   
TACGCAAGATTAGGTTCAAAAGAGTGATGGTTGCTCCGGTTCGTCTGATGACGCTGGCTTATTTGCGCGTAATTTGCGCATTAATCGCTGCCGACAAAGGCGCAGCACCTCTTGTTTTTCGCCATCGCTCATTT  >  minE/1053357‑1053490

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