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 2,893,824 A→G 73.1% E461E (GAA→GAG)  ytfR → predicted sugar transporter subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,893,8240AG73.1% 96.2 / 32.9 85E461E (GAA→GAG) ytfRpredicted sugar transporter subunit
Reads supporting (aligned to +/- strand):  ref base A (8/15);  new base G (29/33);  total (37/48)
Fisher's exact test for biased strand distribution p-value = 4.61e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GAGATCATCCGCCTGATTGAAACGCTATGCGCCGATGGTCTGGCGCTGCTGGTGATCTCCTCCGAACTGGAAGAGCTGGTGGGCTATGCCGATCGGGTGATTATCATGCGCGATCGCAAACAGGTGG  >  minE/2893759‑2893885
                                                                 |                                                             
gagaTCATCCGCCTGATTGAAACGCTATGCGCCGATGGTCTGGCGCTGCTGGTGATCTCCTCCGAACTg                                                            <  1:698795/69‑1 (MQ=255)
 agaTCATCCGCCTGATTGAAACGCTATGCGCCGATGGTCTGGCGCTGCTGGTGATCTCCTCCGAACTgg                                                           <  1:2979296/69‑1 (MQ=255)
   atcatcCGCCTGATTGAAACGCTATGCGCCGATGGTCTGGCGCTGCTGGTGATCTCCTCCGAACTgg                                                           >  1:1858413/1‑67 (MQ=255)
   atcatcCGCCTGATTGAAACGCTATGCGCCGATGGTCTGGCGCTGCTGGTGATCTCCTCCGAACTgg                                                           >  1:305802/1‑67 (MQ=255)
   atcatcCGCCTGATTGAAACGCTATGCGCCGATGGTCTGGCGCTGCTGGTGATCTCCTCCGAACTgg                                                           >  1:1061686/1‑67 (MQ=255)
   atcatcCGCCTGATTGAAACGCTATGCGCCGATGGTCTGGCGCTGCTGGTGATCTCCTCCGAACTgg                                                           >  1:693229/1‑67 (MQ=255)
     catcCGCCTGATTGAAACGCTATGCGCCGATGGTCTGGCGCTGCTGGTGATCTCCTCCGAACTGGAaga                                                       >  1:1277732/1‑69 (MQ=255)
     catcCGCCTGATTGAAACGCTATGCGCCGATGGTCTGGCGCTGCTGGTGATCTCCTCCGAACTGGAaga                                                       >  1:1463999/1‑69 (MQ=255)
                 tGAAAGGCTATGCGCCGATGGTCTGGCGCTGCTGGTGATCTCCTCCGAACTGGAAGAGCTGGTGGGc                                             <  1:243135/67‑1 (MQ=255)
                 tGAAACGCTTTGCGCCGATGGGCTGGCGCTGCTGGTGATCTCCTCCGAGCTGGAAGAGCTGGTGGGCt                                            <  1:3237884/68‑1 (MQ=255)
                 tGAAACGCTGTGCGCCGATGGGCTGGCGCTGCTGGTGATCTCCTCCGAGCTGGAAGAGCTGGTGGGCt                                            <  1:716875/68‑1 (MQ=255)
                 tGAAACGCTGTGCGCCGATGGGCTGGCGCTGCTGGTGATCTCCTCCGAGCTGGAAGAGCTGGTGGGCt                                            <  1:1020656/68‑1 (MQ=255)
                 tGAAACGCTGTGCGCCGATGGGCTGGCGCTGCTGGTGATCTCCTCCGAGCTGGAAGAGCTGGTGGGCt                                            <  1:1954658/68‑1 (MQ=255)
                 tGAAACGCTGTGCGCCGATGGGCTGGCGCTGCTGGTGATCTCCTCCGAGCTGGAAGAGCTGGTGGGCt                                            <  1:2188620/68‑1 (MQ=255)
                 tGAAACGCTGTGCGCCGATGGGCTGGCGCTGCTGGTGATCTCCTCCGAGCTGGAAGAGCTGGTGGGCt                                            <  1:2372208/68‑1 (MQ=255)
                 tGAAACGCTGTGCGCCGATGGGCTGGCGCTGCTGGTGATCTCCTCCGAGCTGGAAGAGCTGGTGGGCt                                            <  1:2838713/68‑1 (MQ=255)
                 tGAAACGCTGTGCGCCGATGGGCTGGCGCTGCTGGTGATCTCCTCCGAGCTGGAAGAGCTGGTGGGCt                                            <  1:2859016/68‑1 (MQ=255)
                 tGAAACGCTGTGCGCCGATGGGCTGGCGCTGCTGGTGATCTCCTCCGAGCTGGAAGAGCTGGTGGGCt                                            <  1:670490/68‑1 (MQ=255)
                 tGAAACGCTGTGCGCCGATGGGCTGGCGCTGCTGGTGATCTCCTCCGAGCTGGAAGAGCTGGTGGGCt                                            <  1:2914920/68‑1 (MQ=255)
                 tGAAACGCTGTGCGCCGATGGGCTGGCGCTGCTGGTGATCTCCTCCGAGCTGGAAGAGCTGGTGGGCt                                            <  1:687467/68‑1 (MQ=255)
                 tGAAACGCTGTGCGCCGATGGGCTGGCGCTGCTGGTGATCTCCTCCGAGCTGGAAGAGCTGGTGGGCt                                            <  1:3187829/68‑1 (MQ=255)
                 tGAAACGCTGTGCGCCGATGGGCTGGCGCTGCTGGTGATCTCCTCCGAGCTGGAAGAGCTGGTGGGCt                                            <  1:3295488/68‑1 (MQ=255)
                 tGAAACGCTGTGCGCCGATGGGCTGGCGCTGCTGGTGATCTCCTCCGAGCTGGAAGAGCTGGTGGGCt                                            <  1:1154625/68‑1 (MQ=255)
                 tGAAACGCTGTGCGCCGATGGGCTGGCGCTGCTGGTGATCTCCTCCGAGCTGGAAGAGCTGGTGGGCt                                            <  1:1269723/68‑1 (MQ=255)
                 tGAAACGCTGTGCGCCGATGGGCTGGCGCTGCTGGTGATCTCCTCCGAGCTGGAAGAGCTGGTGGGCt                                            <  1:1303305/68‑1 (MQ=255)
                 tGAAACGCTGTGCGCCGATGGGCTGGCGCTGCTGGTGATCTCCTCCGAGCTGGAAGAGCTGGTGGGCt                                            <  1:1574258/68‑1 (MQ=255)
                 tGAAACGCTGTGCGCCGATGGGCTGGCGCTGCTGGTGATCTCCTCCGAGCTGGAAGAGCTGGTGGGCt                                            <  1:1561390/68‑1 (MQ=255)
                 tGAAACGCTGTGAGCCGATGGGCTGGCGCTGCTGGTGATCTCCTCCGAGCTGGAAGAGCTGGTGGGCt                                            <  1:2499277/68‑1 (MQ=255)
                 tGAAACGCTATGCGCCGATGGTCTGGCGCTGCTGGTGATCTCCTCCGAACTGGAAGAGCTGGTGGGc                                             <  1:1331387/67‑1 (MQ=255)
                  gAAACGCTGTGCGCCGATGGGCTGGCGCTGCTGGTGATCTCCTCCGAGCTGGAAGAGCTGGTGGGCt                                            <  1:1168696/67‑1 (MQ=255)
                        cTATGCGCCGATGGTCTGGCGCTGCTGGTGATCTCCTCCGAACTGGAAGAGCTGGTGGGCTATGCCGAt                                    >  1:1392749/1‑69 (MQ=255)
                        cTATGCGCCGATGGTCTGGCGCTGCTGGTGATCTCCTCCGAACTGGAAGAGCTGGTGGGCTATGCCGAt                                    >  1:2043350/1‑69 (MQ=255)
                               ccGATGGTCTGGCGCTGCTGGTGATCTCCTCCGAACTGGAAGAGCTGGTGGGCTATGCCg                                      <  1:1474629/60‑1 (MQ=255)
                                   tGGTCTGGCGCTGCTGGTGATCTCCTCCGAACTGGAAGAGCTGGTGGGCTATGCCGATCGGGTGATTAt                         <  1:1722525/69‑1 (MQ=255)
                                   tGGTCTGGCGCTGCTGGTGATCTCCTCCGAACTGGAAGAGCTGGTGGGCTATGCCGATCGGGTGATTAt                         <  1:2821532/69‑1 (MQ=255)
                                   tGGTCTGGCGCTGCTGGTGATCTCCTCCGAACTGGAAGAGCTGGTGGGCTATGCCGATCGGGTGATTAt                         <  1:2337782/69‑1 (MQ=255)
                                   tGGTCTGGCGCTGCTGGTGATCTCCTCCGAACTGGAAGAGCTGGTGGGCTATGCCGATCGGGTGATTAt                         <  1:858732/69‑1 (MQ=255)
                                   tGGTCTGGCGCTGCTGGTGATCTCCTCCGAACTGGAAGAGCTGGTGGGCTATGCCGATCGGGTGATTAt                         <  1:1764059/69‑1 (MQ=255)
                                    ggTCTGGCGCTGCTGGTGATCTCCTCCGAACTGGAAGAGCTGGTGGGCTATGCCGATCGGGTGATTAt                         <  1:3042520/68‑1 (MQ=255)
                                         ggCGCTGCTGGTGATCTCCTCCGAGCTGGAAGAGCTGGTGGGCt                                            <  1:1517539/44‑1 (MQ=255)
                                                  ggTGATCTCCTCCGAACTGGAAGAGCTGGTGGGCTATGCCGATCGGGTGATTATCATGCGCGATCGCa           <  1:2127107/68‑1 (MQ=255)
                                                  ggTGATCTCCTCCGAACTGGAAGAGCTGGTGGGCTATGCCGATCGGGTGATTATCATGCGCGATCGCa           <  1:508889/68‑1 (MQ=255)
                                                  ggTGATCTCCTCCGAACTGGAAGAGCTGGTGGGCTATGCCGATCGGGTGATTATCATGCGCGATCGCa           <  1:500275/68‑1 (MQ=255)
                                                  ggTGATCTCCTCCGAACTGGAAGAGCTGGTGGGCTATGCCGATCGGGTGATTATCATGCGCGATCGCa           <  1:1976704/68‑1 (MQ=255)
                                                      aTCTCCTCCGAGCTGGAAGAGCTGGTGGGCTATGGCGATCGGGTGATTATCATGCGCGATCGCAAACAg      >  1:586125/1‑69 (MQ=255)
                                                      aTCTCCTCCGAGCTGGAAGAGCTGGTGGGCTATGCCGATCGGGTGATTATCATGCGCGATCGCAAACAg      >  1:425767/1‑69 (MQ=255)
                                                      aTCTCCTCCGAGCTGGAAGAGCTGGTGGGCTATGCCGATCGGGTGATTATCATGCGCGATCGCAAACAg      >  1:3103619/1‑69 (MQ=255)
                                                      aTCTCCTCCGAGCTGGAAGAGCTGGTGGGCTATGCCGATCGGGTGATTATCATGCGCGATCGCAAACAg      >  1:924536/1‑69 (MQ=255)
                                                      aTCTCCTCCGAGCTGGAAGAGCTGGTGGGCTATGCCGATCGGGTGATTATCATGCGCGATCGCAAACAg      >  1:1224265/1‑69 (MQ=255)
                                                      aTCTCCTCCGAGCTGGAAGAGCTGGTGGGCTATGCCGATCGGGTGATTATCATGCGCGATCGCAAACAg      >  1:3200691/1‑69 (MQ=255)
                                                      aTCTCCTCCGAGCTGGAAGAGCTGGTGGGCTATGCCGATCGGGTGATTATCATGCGCGATCGCAAACAg      >  1:1698263/1‑69 (MQ=255)
                                                      aTCTCCTCCGAGCTGGAAGAGCTGGTGGGCTATGCCGATCGGGTGATTATCATGCGCGATCGCAAACAg      >  1:696973/1‑69 (MQ=255)
                                                      aTCTCCTCCGAGCTGGAAGAGCTGGTGGGCTATGCCGATCGGGTGATTATCATGCGCGATCGCAAACAg      >  1:2232596/1‑69 (MQ=255)
                                                      aTCTCCTCCGAGCTGGAAGAGCTGGTGGGCTATGCCGATCGGGTGATTATCATGCGCGATCGCAAACAg      >  1:500399/1‑69 (MQ=255)
                                                      aTCTCCTCCGAGCTGGAAGAGCTGGTGGGCTATGCCGATCGGGTGATTATCATGCGCGATCGCAAACAg      >  1:60729/1‑69 (MQ=255)
                                                      aTCTCCTCCGAGCTGGAAGAGCTGGTGGGCTATGCCGATCGGGTGATTATCATGCGCGATCGCAAACAg      >  1:1128654/1‑69 (MQ=255)
                                                      aTCTCCTCCGAGCTGGAAGAGCTGGTGGGCTATGCCGATCGGGTGATTATCATGCGCGATCGCAAACAg      >  1:962696/1‑69 (MQ=255)
                                                      aTCTCCTCCGAGCTGGAAGAGCTGGTGGGCTATGCCGATCGGGTGATTATCATGCGCGATCGCAAACAg      >  1:3039624/1‑69 (MQ=255)
                                                      aTCTCCTCCGAGCTGGAAGAGCTGGTGGGCTATGCCGATCGGGTGATTATCATGCGCGATCGCAAACAg      >  1:2241384/1‑69 (MQ=255)
                                                      aTCTCCTCCGAGCTGGAAGAGCTGGTGGGCTATGCCGATCGGGTGATTATCATGCGCGATCGCAAACAg      >  1:826707/1‑69 (MQ=255)
                                                      aTCTCCTCCGAGCTGGAAGAGCTGGTGGGCTATGCCGATCGGGTGATTATCATGCGCGATCGCAAACAg      >  1:258597/1‑69 (MQ=255)
                                                      aTCTCCTCCGAGCTGGAAGAGCTGGTGGGCTATGCCGATCGGGTGATTATCATGCGCGATCGCAAACAg      >  1:2649471/1‑69 (MQ=255)
                                                      aTCTCCTCCGAGCTGGAAGAGCTGGTGGGCTATGCCGATCGGGTGATTATCATGCGCGATCGCAAACAg      >  1:2694367/1‑69 (MQ=255)
                                                      aTCTCCTCCGAGCTGGAAGAGCTGGTGGGCTATGCCGATCGGGTGATTATCATGCGCGATCGCAAACAg      >  1:814862/1‑69 (MQ=255)
                                                      aTCTCCTCCGAGCTGGAAGAGCTGGTGGGCTATGCCGATCGGGTGATTATCATGCGCGATCGCAAACAg      >  1:208698/1‑69 (MQ=255)
                                                      aTCTCCTCCGAGCTGGAAGAGCTGGTGGGCTATGCCGATCGGGTGATTATCATGCGCGATCGCAAACAg      >  1:2053380/1‑69 (MQ=255)
                                                      aTCTCCTCCGAGCTGGAAGAGCTGGTGGGCTATGCCGATCGGGTGATTATCATGCGCGATCGCAAACAg      >  1:913178/1‑69 (MQ=255)
                                                      aTCTCCTCCGAGCTGGAAGAGCTGGTGGGCTATGCCGATCGGGTGATTATCATGCGCGATCGCAAACAg      >  1:771319/1‑69 (MQ=255)
                                                      aTCTCCTCCGAGCTGGAAGAGCTGGTGGGCTATGCCGATCGGGTGATTATCATGCGCGATCGCAAACAg      >  1:1313213/1‑69 (MQ=255)
                                                      aTCTCCTCCGAGCTGGAAGAGCTGGTGGGCTATGCCGATCGGGTGATTATCATGCGCGATCGCAAACAg      >  1:130908/1‑69 (MQ=255)
                                                      aTCTCCTCCGAGCTGGAAGAGCTGGTGGGCTATGCCGATCGGGTGATTATCATGCGCGATCGCAAACAg      >  1:3022413/1‑69 (MQ=255)
                                                      aTCTCCTCCGAGCTGGAAGAGCTGGTGGGCTATGCCGATCGGGTGATTATCATGCGCGATCGCAAACAg      >  1:1876816/1‑69 (MQ=255)
                                                      aTCTCCTCCGAGATGGAAGAGCTGGTGGGCTATGCCGATCGGGTGATTATCATGCGCGATCGCAAACAg      >  1:1537048/1‑69 (MQ=255)
                                                             ccGAGCTGGAAGAGCTGGTGGGCTATGCCGATCGGGTGATTATCATGCGCGATCGCAAACAGGTgg  <  1:988738/66‑1 (MQ=255)
                                                             ccGAGCTGGAAGAGCTGGTGGGCTATGCCGATCGGGTGATTATCATGCGCGATCGCAAACAGGTgg  <  1:375209/66‑1 (MQ=255)
                                                             ccGAGCTGGAAGAGCTGGTGGGCTATGCCGATCGGGTGATTATCATGCGCGATCGCAAACAGGTgg  <  1:318256/66‑1 (MQ=255)
                                                             ccGAGCTGGAAGAGCTGGTGGGCTATGCCGATCGGGTGATTATCATGCGCGATCGCAAACAGGTgg  <  1:2913586/66‑1 (MQ=255)
                                                             ccGAGCTGGAAGAGCTGGTGGGCTATGCCGATCGGGTGATTATCATGCGCGATCGCAAACAGGTgg  <  1:2907315/66‑1 (MQ=255)
                                                             ccGAGCTGGAAGAGCTGGTGGGCTATGCCGATCGGGTGATTATCATGCGCGATCGCAAACAGGTgg  <  1:2819000/66‑1 (MQ=255)
                                                             ccGAGCTGGAAGAGCTGGTGGGCTATGCCGATCGGGTGATTATCATGCGCGATCGCAAACAGGTgg  <  1:2409115/66‑1 (MQ=255)
                                                             ccGAGCTGGAAGAGCTGGTGGGCTATGCCGATCGGGTGATTATCATGCGCGATCGCAAACAGGTgg  <  1:2258003/66‑1 (MQ=255)
                                                             ccGAGCTGGAAGAGCTGGTGGGCTATGCCGATCGGGTGATTATCATGCGCGATCGCAAACAGGTgg  <  1:2020887/66‑1 (MQ=255)
                                                             ccGAGCTGGAAGAGCTGGTGGGCTATGCCGATCGGGTGATTATCATGCGCGATCGCAAACAGGTgg  <  1:1631352/66‑1 (MQ=255)
                                                             ccGAGCTGGAAGAGCTGGTGGGCTATGCCGATCGGGTGATTATCATGCGCGATCGCAAACAGGTgg  <  1:1115400/66‑1 (MQ=255)
                                                             ccGAGCTGGAAGAGCTGGTGGGCTATGCCGATCGGGTGATTATCATGCGCGATCGCAAACAGGTgg  <  1:1036213/66‑1 (MQ=255)
                                                                 |                                                             
GAGATCATCCGCCTGATTGAAACGCTATGCGCCGATGGTCTGGCGCTGCTGGTGATCTCCTCCGAACTGGAAGAGCTGGTGGGCTATGCCGATCGGGTGATTATCATGCGCGATCGCAAACAGGTGG  >  minE/2893759‑2893885

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