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 2,753,813 A→C 57.2% D63E (GAT→GAG)  mscL ← mechanosensitive channel

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,753,8130AC57.2% 56.9 / 98.8 105D63E (GAT→GAG) mscLmechanosensitive channel
Reads supporting (aligned to +/- strand):  ref base A (19/26);  new base C (42/18);  total (61/44)
Fisher's exact test for biased strand distribution p-value = 5.36e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.33e-01

Only 100 of 111 total aligned reads displayed.

AAATCAAAGACGTTTTGAATGAAGACACCGTAATGCATCACAACAGCAGGGATATCCCCCTGCGCATCGCGTAGCGTGACAGCAAACTGTTTAAAATCGATCCCGCCAATTAATAAGCCCAGAGGAGGCATGAT  >  minE/2753748‑2753881
                                                                 |                                                                    
aaaTCAAAGACGTTTTGAATGAAGACACCGTAATGCATCACAACAGCAGGGATATCCCCCTGCGCATcg                                                                   >  1:202933/1‑69 (MQ=255)
aaaTCAAAGACGTTTTGAATGAAGACACCGTAATGCATCACAACAGCAGGGATATCCCCCTGCGCATcg                                                                   >  1:771741/1‑69 (MQ=255)
                                aTGCATCACAACAGCAGGGATATCCCCTTGGGCCTCGCGTAGCGTGACAGCAAACTGTTTAAAGTCGAt                                   <  1:2363059/69‑1 (MQ=255)
                                aTGCATCACAACAGCAGGGATATCCCCTTGGGCCTCGCGTAGCGTGACAGCAAACTGTTTAAAGTCGAt                                   <  1:1887045/69‑1 (MQ=255)
                                aTGCATCACAACAGCAGGGATATCCCCTTGGGCCTCGCGTAGCGTGACAGCAAACTGTTTAAAGTCGAt                                   <  1:1809671/69‑1 (MQ=255)
                                aTGCATCACAACAGCAGGGATATCCCCTTGGGCCTCGCGTAGCGTGACAGCAAACTGTTTAAAGTCGAt                                   <  1:1911233/69‑1 (MQ=255)
                                aTGCATCACAACAGCAGGGATATCCCCTTGGGCCTCGCGTAGCGTGACAGCAAACTGTTTAAAGTCGAt                                   <  1:1787056/69‑1 (MQ=255)
                                aTGCATCACAACAGCAGGGATATCCCCTTGGGCCTCGCGTAGCGTGACAGCAAACTGTTTAAAGTCGAt                                   <  1:17313/69‑1 (MQ=255)
                                aTGCATCACAACAGCAGGGATATCCCCTTGGGCCTCGCGTAGCGTGACAGCAAACTGTTTAAAGTCGAt                                   <  1:222999/69‑1 (MQ=255)
                                aTGCATCACAACAGCAGGGATATCCCCTTGGGCCTCGCGTAGCGTGACAGCAAACTGTTTAAAGTCGAt                                   <  1:1698139/69‑1 (MQ=255)
                                aTGCATCACAACAGCAGGGATATCCCCTTGGGCCTCGCGTAGCGTGACAGCAAACTGTTTAAAGTCGAt                                   <  1:3109143/69‑1 (MQ=255)
                                aTGCATCACAACAGCAGGGATATCCCCTTGGGCCTCGCGTAGCGTGACAGCAAACTGTTTAAAGTCGAt                                   <  1:2412593/69‑1 (MQ=255)
                                aTGCATCACAACAGCAGGGATATCCCCTTGGGCCTCGCGTAGCGTGACAGCAAACTGTTTAAAGTCGAt                                   <  1:2420274/69‑1 (MQ=255)
                                aTGCATCACAACAGCAGGGATATCCCCTTGGGCCTCGCGTAGCGTGACAGCAAACTGTTTAAAGTCGAt                                   <  1:791622/69‑1 (MQ=255)
                                aTGCATCACAACAGCAGGGATATCCCCTTGGGCCTCGCGTAGCGTGACAGCAAACTGTTTAAAGTCGAt                                   <  1:2829578/69‑1 (MQ=255)
                                aTGCATCACAACAGCAGGGATATCCCCTTGGGCCTCGCGTAGCGTGACAGCAAACTGTTTAAAGTCGAt                                   <  1:1366996/69‑1 (MQ=255)
                                aTGCATCACAACAGCAGGGATATCCCCTTGGGCCTCGCGTAGCGTGACAGCAAACTGTTTAAAGTCGAt                                   <  1:2604256/69‑1 (MQ=255)
                                 tGCATCACAACAGCAGGGATATCCCCTTGGGCCTCGCGTAGCGTGACAGCAAACTGTTTAAAGTCGAt                                   <  1:1927730/68‑1 (MQ=255)
                                     tCACAACAGCAGGGATATCCCCCTGCGCATCGCGTAGCGTGACAGCAAACTGTTTAAAATCGATCCCGc                              <  1:1727264/69‑1 (MQ=255)
                                     tCACAACAGCAGGGATATCCCCCTGCGCATCGCGTAGCGTGACAGCAAACTGTTTAAAATCGATCCCGc                              <  1:2426428/69‑1 (MQ=255)
                                     tCACAACAGCAGGGATATCCCCCTGCGCATCGCGTAGCGTGACAGCAAACTGTTTAAAATCGATCCCGc                              <  1:260367/69‑1 (MQ=255)
                                     tCACAACAGCAGGGATATCCCCCTGCGCATCGCGTAGCGTGACAGCAAACTGTTTAAAATCGATCCCGc                              <  1:2709887/69‑1 (MQ=255)
                                       acaacaGCAGGGATATCCCCCTGCGCATCGCGTAGCGTGACAGCAAACTGTTTAAAATc                                      <  1:3226234/59‑1 (MQ=255)
                                       acaacaGCAGGGATATCCCCCTGCGCATCGCGTAGCGTGACAGCAAACTGTTTAAAATCGATCCCGCCa                            >  1:2248810/1‑69 (MQ=255)
                                       acaacaGCAGGGATATCCCCCTGCGCATCGCGTAGCGTGACAGCAAACTGTTTAAAATCGATCCCGCCa                            >  1:1012416/1‑69 (MQ=255)
                                       acaacaGCAGGGATATCCCCCTGCGCATCGCGTAGCGTGACAGCAAACTGTTTAAAATCGATCCCGCCa                            >  1:176653/1‑69 (MQ=255)
                                       acaacaGCAGGGATATCCCCCTGCGCATCGCGTAGCGTGACAGCAAACTGTTTAAAATCGATCCCGCCa                            >  1:630632/1‑69 (MQ=255)
                                       acaacaGCAGGGATATCCCCCTGCGCATCGCGTAGCGTGACAGCAAACTGTTTAAAATCGATCCCGCCa                            >  1:1085953/1‑69 (MQ=255)
                                       acaacaGCAGGGATATCCCCCTGCGCATCGCGTAGCGTGACAGCAAACTGTTTAAAATCGATCCCGCCa                            >  1:1082016/1‑69 (MQ=255)
                                        caacaGCAGGGATATCCCCCTGCGCATCGCGTAGCGTGACAGCAAACTGTTTAAAATc                                      <  1:177629/58‑1 (MQ=255)
                                                   atatCCCCTTGGGCCTCGCGTAGCGTGACAGCAAACTGTTTAAAGTCGATCCCGCCAATtaataa                    >  1:1438463/1‑65 (MQ=255)
                                                   atatCCCCTTGGGCCTCGCGTAGCGTGACAGCAAACTGTTTAAAGTCGATCCCGCCAATtaataa                    >  1:1068595/1‑65 (MQ=255)
                                                   atatCCCCTTGGGCCTCGCGTAGCGTGACAGCAAACTGTTTAAAGTCGATCCCGCCAATTAATAAg                   >  1:2273260/1‑66 (MQ=255)
                                                   atatCCCCTTGGGCCTCGCGTAGCGTGACAGCAAACTGTTTAAAGTCGATCCCGCCAATTAATAAg                   >  1:2770214/1‑66 (MQ=255)
                                                   atatCCCCTTGGGCCTCGCGTAGCGTGACAGCAAACTGTTTAAAGTCGATCCCGCCAATTAATAAg                   >  1:279107/1‑66 (MQ=255)
                                                   atatCCCCTTGGGCCTCGCGTAGCGTGACAGCAAACTGTTTAAAGTCGATCCCGCCAATTAATAAg                   >  1:845808/1‑66 (MQ=255)
                                                   atatCCCCTTGGGCCTCGCGTAGCGTGACAGCAAACTGTTTAAAGTCGATCCCGCCAATTAATAAg                   >  1:453725/1‑66 (MQ=255)
                                                   atatCCCCTTGGGCCTCGCGTAGCGTGACAGCAAACTGTTTAAAGTCGATCCCGCCAATTAATAAg                   >  1:1230760/1‑66 (MQ=255)
                                                   atatCCCCTTGGGCCTCGCGTAGCGTGACAGCAAACTGTTTAAAGTCGATCCCGCCAATTAATAAg                   >  1:1554419/1‑66 (MQ=255)
                                                   atatCCCCTTGGGCCTCGCGTAGCGTGACAGCAAACTGTTTAAAGTCGATCCCGCCAATTAATAAg                   >  1:1563166/1‑66 (MQ=255)
                                                   atatCCCCTTGGGCCTCGCGTAGCGTGACAGCAAACTGTTTAAAGTCGATCCCGCCAATTAATAAg                   >  1:1571181/1‑66 (MQ=255)
                                                   atatCCCCTTGGGCCTCGCGTAGCGTGACAGCAAACTGTTTAAAGTCGATCCCGCCAATTAATAAg                   >  1:1698815/1‑66 (MQ=255)
                                                   atatCCCCTTGGGCCTCGCGTAGCGTGACAGCAAACTGTTTAAAGTCGATCCCGCCAATTAATAAg                   >  1:1199113/1‑66 (MQ=255)
                                                   atatCCCCTTGGGCCTCGCGTAGCGTGACAGCAAACTGTTTAAAGTCGATCCCGCCAATTAATAAg                   >  1:421547/1‑66 (MQ=255)
                                                   atatCCCCCTGCGCATCGCGTAGCGTGACAGCAAACTGTTTAAAATCGATCCCGCCAATTAATAAg                   >  1:1524146/1‑66 (MQ=255)
                                                   atatCCCCCTGCGCATCGCGTAGCGTGACAGCAAACTGTTTAAAATCGATCCCGCCAATTAATAAg                   >  1:1484586/1‑66 (MQ=255)
                                                   atatCCCCCTGCGCATCGCGTAGCGTGACAGCAAACTGTTTAAAATCGATCCCGCCAATTAATAAg                   >  1:143927/1‑66 (MQ=255)
                                                    tatCCCCTTGGGCCTCGCGTAGCGTGACAGCAAACTGTTTAAAGTc                                      >  1:2071036/1‑46 (MQ=255)
                                                    tatCCCCTTGGGCCTCGCGTAGCGTGACAGCAAACTGTTTAAAGTCGATCCCGcc                             >  1:610389/1‑55 (MQ=255)
                                                    tatCCCCTTGGGCCTCGCGTAGCGTGACAGCAAACTGTTTAAAGTCGATCCCGc                              >  1:618140/1‑54 (MQ=255)
                                                    tatCCCCTTGGGCCTCGCGTAGCGTGACAGCAAACTGTTTAAAGTCGATCCCGCCa                            >  1:1178198/1‑56 (MQ=255)
                                                    tatCCCCTTGGGCCTCGCGTAGCGTGACAGCAAACTGTTTAAAGTCGATCCCGCCa                            >  1:29370/1‑56 (MQ=255)
                                                    tatCCCCTTGGGCCTCGCGTAGCGTGACAGCAAACTGTTTAAAGTCGATCCCGCCa                            >  1:2809482/1‑56 (MQ=255)
                                                    tatCCCCTTGGGCCTCGCGTAGCGTGACAGCAAACTGTTTAAAGTCGATCCCGCCa                            >  1:83458/1‑56 (MQ=255)
                                                    tatCCCCTTGGGCCTCGCGTAGCGTGACAGCAAACTGTTTAAAGTCGATCCCGCCa                            >  1:292010/1‑56 (MQ=255)
                                                    tatCCCCTTGGGCCTCGCGTAGCGTGACAGCAAACTGTTTAAAGTCGATCCCGCCa                            >  1:2948851/1‑56 (MQ=255)
                                                    tatCCCCTTGGGCCTCGCGTAGCGTGACAGCAAACTGTTTAAAGTCGATCCCGCCa                            >  1:2983074/1‑56 (MQ=255)
                                                    tatCCCCTTGGGCCTCGCGTAGCGTGACAGCAAACTGTTTAAAGTCGATCCCGCCa                            >  1:2604650/1‑56 (MQ=255)
                                                    tatCCCCTTGGGCCTCGCGTAGCGTGACAGCAAACTGTTTAAAGTCGATCCCGCCa                            >  1:288174/1‑56 (MQ=255)
                                                    tatCCCCTTGGGCCTCGCGTAGCGTGACAGCAAACTGTTTAAAGTCGATCCCGCCa                            >  1:1310764/1‑56 (MQ=255)
                                                    tatCCCCTTGGGCCTCGCGTAGCGTGACAGCAAACTGTTTAAAGTCGATCCCGCCa                            >  1:1368290/1‑56 (MQ=255)
                                                    tatCCCCTTGGGCCTCGCGTAGCGTGACAGCAAACTGTTTAAAGTCGATCCCGCCa                            >  1:3041500/1‑56 (MQ=255)
                                                    tatCCCCTTGGGCCTCGCGTAGCGTGACAGCAAACTGTTTAAAGTCGATCCCGCCa                            >  1:2323586/1‑56 (MQ=255)
                                                    tatCCCCTTGGGCCTCGCGTAGCGTGACAGCAAACTGTTTAAAGTCGATCCCGCCa                            >  1:1655386/1‑56 (MQ=255)
                                                    tatCCCCTTGGGCCTCGCGTAGCGTGACAGCAAACTGTTTAAAGTCGATCCCGCCa                            >  1:2058074/1‑56 (MQ=255)
                                                    tatCCCCTTGGGCCTCGCGTAGCGTGACAGCAAACTGTTTAAAGTCGATCCCGCCa                            >  1:1778979/1‑56 (MQ=255)
                                                    tatCCCCTTGGGCCTCGCGTAGCGTGACAGCAAACTGTTTAAAGTCGATCCCGCCa                            >  1:1929944/1‑56 (MQ=255)
                                                    tatCCCCTTGGGCCTCGCGTAGCGTGACAGCAAACTGTTTAAAGTCGATCCCGCCa                            >  1:617748/1‑56 (MQ=255)
                                                    tatCCCCTTGGGCCTCGCGTAGCGTGACAGCAAACTGTTTAAAGTCGATCCCGCCa                            >  1:1905614/1‑56 (MQ=255)
                                                    tatCCCCTTGGGCCTCGCGTAGCGTGACAGCAAACTGTTTAAAGTCGATCCCGCCa                            >  1:3350713/1‑56 (MQ=255)
                                                      tCCCCCTGCGCATCGCGTAGCGTGACAGCAAACTGTTTAAAATCGa                                    <  1:2307930/46‑1 (MQ=255)
                                                      tCCCCCTGCGCATCGCGTAGCGTGACAGCAAACTGTTTAAAATCGa                                    <  1:2332477/46‑1 (MQ=255)
                                                      tCCCCCTGCGCATCGCGTAGCGTGACAGCAAACTGTTTAAAATCGATCCCGCCAAtt                         >  1:3398657/1‑57 (MQ=255)
                                                      tCCCCCTGCGCATCGCGTAGCGTGACAGCAAACTGTTTAAAATCGATCCCGCCAAtt                         >  1:103602/1‑57 (MQ=255)
                                                      tCCCCCTGCGCATCGCGTAGCGTGACAGCAAACTGTTTAAAATCGATCCCGCCAAtt                         >  1:678761/1‑57 (MQ=255)
                                                      tCCCCCTGCGCATCGCGTAGCGTGACAGCAAACTGTTTAAAATCGATCCCGCCAAtt                         >  1:1787501/1‑57 (MQ=255)
                                                      tCCCCCTGCGCATCGCGTAGCGTGACAGCAAACTGTTTAAAATCGATCCCGCCAAtt                         >  1:339220/1‑57 (MQ=255)
                                                      tCCCCCTGCGCATCGCGTAGCGTGACAGCAAACTGTTTAAAATCGATCCCGCCAAtt                         >  1:3325720/1‑57 (MQ=255)
                                                      tCCCCCTGCGCATCGCGTAGCGTGACAGCAAACTGTTTAAAATCGATCCCGCCAAtt                         >  1:2607403/1‑57 (MQ=255)
                                                           cTGCGCATCGCGTAGCGTGACAGCAAACTGTTTAAAATCGATCCCGCCAATTAATAAGCCCAGaggagg        <  1:3111680/69‑1 (MQ=255)
                                                           cTGCGCATCGCGTAGCGTGACAGCAAACTGTTTAAAATCGATCCCGCCAATTAATAAGCCCAGaggagg        <  1:1200292/69‑1 (MQ=255)
                                                           cTGCGCATCGCGTAGCGTGACAGCAAACTGTTTAAAATCGATCCCGCCAATTAATAAGCCCAGaggagg        <  1:1887876/69‑1 (MQ=255)
                                                           cTGCGCATCGCGTAGCGTGACAGCAAACTGTTTAAAATCGATCCCGCCAATTAATAAGCCCAGaggagg        <  1:1306254/69‑1 (MQ=255)
                                                           cTGCGCATCGCGTAGCGTGACAGCAAACTGTTTAAAATCGATCCCGCCAATTAATAAGCCCAGaggagg        <  1:3399698/69‑1 (MQ=255)
                                                           cTGCGCATCGCGTAGCGTGACAGCAAACTGTTTAAAATCGATCCCGCCAATTAATAAGCCCAGaggagg        <  1:369879/69‑1 (MQ=255)
                                                           cTGCGCATCGCGTAGCGTGACAGCAAACTGTTTAAAATCGATCCCGCCAATTAATAAGCCCAGaggagg        <  1:1784619/69‑1 (MQ=255)
                                                            tGCGCATCGCGTAGCGTGACAGCAAACTGTTTAAAATCGATCCCGCCAATTAATAAGcc                 <  1:2235129/59‑1 (MQ=255)
                                                            tGCGCATCGCGTAGCGTGACAGCAAACTGTTTAAAATCGATCCCGCCAATTAATAAGcc                 <  1:289136/59‑1 (MQ=255)
                                                             gcgcATCGCGTAGCGTGACAGCAAACTGTTTAAAATCGATCCCGCCAATTAATAAGCCCAGAGGAGGCa      <  1:1835626/69‑1 (MQ=255)
                                                             gcgcATCGCGTAGCGTGACAGCAAACTGTTTAAAATCGATCCCGCCAATTAATAAGCCCAGAGGAGGCa      <  1:499097/69‑1 (MQ=255)
                                                             gcgcATCGCGTAGCGTGACAGCAAACTGTTTAAAATCGATCCCGCCAATTAATAAGCCCAGAGGAGGCa      <  1:2353779/69‑1 (MQ=255)
                                                             gcgcATCGCGTAGCGTGACAGCAAACTGTTTAAAATCGATCCCGCCAATTAATAAGCCCAGAGGAGGCa      <  1:1862907/69‑1 (MQ=255)
                                                             gcgcATCGCGTAGCGTGACAGCAAACTGTTTAAAATCGATCCCGCCAATTAATAAGCCCAGAGGAGGCa      <  1:2968048/69‑1 (MQ=255)
                                                             gcgcATCGCGTAGCGTGACAGCAAACTGTTTAAAATCGATCACGCCAATTAATAAGCCCAGAGGAGGCa      <  1:3164600/69‑1 (MQ=255)
                                                                 aTCGCGTAGCGTGACAGCAAACTGTTTAAAATCGATCCCGCCAATTAATAAGCCCAGAGGAGGCatgat  <  1:2637219/69‑1 (MQ=255)
                                                                 aTCGCGTAGCGTGACAGCAAACTGTTTAAAATCGATCCCGCCAATTAATAAGCCCAGAGGAGGCatgat  <  1:1473872/69‑1 (MQ=255)
                                                                 aTCGCGTAGCGTGACAGCAAACTGTTTAAAATCGATCCCGCCAATTAATAAGCCCAGAGGAGGCatgat  <  1:2769203/69‑1 (MQ=255)
                                                                 aTCGCGTAGCGTGACAGCAAACTGTTTAAAATCGATCCCGCCAATTAATAAGCCCAGAGGAGGCatgat  <  1:1211781/69‑1 (MQ=255)
                                                                 aTCGCGTAGCGTGACAGCAAACTGTTTAAAATCGATCCCGCCAATTAATAAGCCCAGAGGAGGCatgat  <  1:2813147/69‑1 (MQ=255)
                                                                 aTCGCGTAGCGTGACAGCAAACTGTTTAAAATCGATCCCGCCAATTAATAAGCCCAGAGGAGGCataat  <  1:1363983/69‑1 (MQ=255)
                                                                 |                                                                    
AAATCAAAGACGTTTTGAATGAAGACACCGTAATGCATCACAACAGCAGGGATATCCCCCTGCGCATCGCGTAGCGTGACAGCAAACTGTTTAAAATCGATCCCGCCAATTAATAAGCCCAGAGGAGGCATGAT  >  minE/2753748‑2753881

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