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 2,409,828 T→C 57.2% I94I (ATT→ATC)  hemX → uroporphyrinogen III methylase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,409,8280TC57.2% 19.2 / 44.9 63I94I (ATT→ATC) hemXuroporphyrinogen III methylase
Reads supporting (aligned to +/- strand):  ref base T (10/17);  new base C (20/16);  total (30/33)
Fisher's exact test for biased strand distribution p-value = 2.03e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CAACTGACGGCATTGCAAAAAGCCCAGGAGAGCCAAAAAGCCGAGCTGGAAGGCATTATTAAGCAACAAGCTGCACAACTTAAGCAGGCGAATCGTCAGCAAGAAACGCTGGCAAAACAGTTGGA  >  minE/2409769‑2409893
                                                           |                                                                 
cAACTGACGGCATTGCGAAAAGCCCAGGAGAGCCAAAAAGCCGAGCTGGAAGGCATTATTAAGcaacaa                                                          <  1:837697/69‑1 (MQ=255)
cAACTGACGGCATTGCAAAAAGCCCAGGAGAGCCAAAAAGCCGAGCTGGAAGGCATTATTAAGcaacaa                                                          <  1:3046306/69‑1 (MQ=255)
    tGACGGCATTGCAAAAAGCCCAGGAGAGCCAAAAAGCCGAGCTGGAAGGCATTATTAAGCAACAAGCTg                                                      <  1:2507889/69‑1 (MQ=255)
    tGACGGCATTGCAAAAAGCCCAGGAGAGCCAAAAAGCCGAGCTGGAAGGCATTATTAAGCAACAAGCTg                                                      <  1:2789063/69‑1 (MQ=255)
    tGACGGCATTGCAAAAAGCCCAGGAGAGCCAAAAAGCCGAGCTGGAAGGCATTATTAAGCAACAAGCTg                                                      <  1:2172544/69‑1 (MQ=255)
    tGACGGCATTGCAAAAAGCCCAGGAGAGCCAAAAAGCCGAGCTGGAAGGCATTATTAAGCAACAAGCTg                                                      <  1:209229/69‑1 (MQ=255)
              gCAAAAAGCCCAGGAGAGCCAAAAAGCCGAGCTGGAAGGCATTATTAAGCAACAAGCTGCACAACTTa                                             >  1:3202760/1‑68 (MQ=255)
                aaaaaGCCCAGGAGAGCCAAAAAGCCGAGCTGGAAGGCATTATTAAGCAACAAGCTGCACAACTTAAg                                           <  1:1004347/68‑1 (MQ=255)
                aaaaaGCCCAGGAGAGCCAAAAAGCCGAGCTGGAAGGCATTATTAAGCAACAAGCTGCACAACTTAAg                                           <  1:1648656/68‑1 (MQ=255)
                aaaaaGCCCAGGAGAGCCAAAAAGCCGAGCTGGAAGGCATTATTAAGCAACAAGCTGCACAACTTAAg                                           <  1:1143844/68‑1 (MQ=255)
                      cccAGGAGAGCCAAAAAGCCGAGCTGGAAGGCATTATTAAGGAACAAGCTGCACAACTTAAGCAGGCGa                                    <  1:1747263/69‑1 (MQ=255)
                      cccAGGAGAGCCAAAAAGCCGAGCTGGAAGGCATTATTAAGCAACAAGCTGCACAACTTAAGCAGGCGa                                    <  1:1285303/69‑1 (MQ=255)
                      cccAGGAGAGCCAAAAAGCCGAGCTGGAAGGCATTATTAAGCAACAAGCTGCACAACTTAAGCAGGCGa                                    <  1:1249430/69‑1 (MQ=255)
                      cccAGGAGAGCCAAAAAGCCGAGCTGGAAGGCATTATTAAGCAACAAGCTGCACAACTTAAGCAGGCGa                                    <  1:3266696/69‑1 (MQ=255)
                      cccAGGAGAGCCAAAAAGCCGAGCTGGAAGGCATTATTAAGCAACAAGCTGCACAACTTAAGCAGGCGa                                    <  1:3076056/69‑1 (MQ=255)
                      cccAGGAGAGCCAAAAAGCCGAGCTGGAAGGCATTATTAAGCAACAAGCTGCACAACTTAAGCAGGCGa                                    <  1:2607918/69‑1 (MQ=255)
                         agcagagCCAAAAAGCCGAGCTGGAAGGCATTATCAAGCAACAAGCTGTACAGCTTGAGCAGGCGAATc                                 >  1:598482/4‑69 (MQ=255)
                         aGGAGAGCCAAAAAGCCGAGCTGGAAGGCATTATCAAGCAACAAGCTGTACAGCTTGAGCAGGCGAAt                                  >  1:1706826/1‑68 (MQ=255)
                         aGGAGAGCCAAAAAGCCGAGCTGGAAGGCATTATCAAGCAACAAGCTGTACAGCTTGAGCAGGCGAATc                                 >  1:2794562/1‑69 (MQ=255)
                         aGGAGAGCCAAAAAGCCGAGCTGGAAGGCATTATCAAGCAACAAGCTGTACAGCTTGAGCAGGCGAATc                                 >  1:1891820/1‑69 (MQ=255)
                         aGGAGAGCCAAAAAGCCGAGCTGGAAGGCATTATCAAGCAACAAGCTGTACAGCTTGAGCAGGCGAATc                                 >  1:3098413/1‑69 (MQ=255)
                         aGGAGAGCCAAAAAGCCGAGCTGGAAGGCATTATCAAGCAACAAGCTGTACAGCTTGAGCAGGCGAATc                                 >  1:2307181/1‑69 (MQ=255)
                         aGGAGAGCCAAAAAGCCGAGCTGGAAGGCATTATCAAGCAACAAGCTGTACAGCTTGAGCAGGCGAATc                                 >  1:2739578/1‑69 (MQ=255)
                         aGGAGAGCCAAAAAGCCGAGCTGGAAGGCATTATCAAGCAACAAGCTGTACAGCTTGAGCAGGCGAATc                                 >  1:2411333/1‑69 (MQ=255)
                         aGGAGAGCCAAAAAGCCGAGCTGGAAGGCATTATCAAGCAACAAGCTGTACAGCTTGAGCAGGCGAATc                                 >  1:2419965/1‑69 (MQ=255)
                         aGGAGAGCCAAAAAGCCGAGCTGGAAGGCATTATCAAGCAACAAGCTGTACAGCTTGAGCAGGCGAATc                                 >  1:2134239/1‑69 (MQ=255)
                         aGGAGAGCCAAAAAGCCGAGCTGGAAGGCATTATCAAGCAACAAGCTGTACAGCTTGAGCAGGCGAATc                                 >  1:2098819/1‑69 (MQ=255)
                         aGGAGAGCCAAAAAGCCGAGCTGGAAGGCATTATCAAGCAACAAGCTGTACAGCTTGAGCAGGCGAATc                                 >  1:3330100/1‑69 (MQ=255)
                         aGGAGAGCCAAAAAGCCGAGCTGGAAGGCATTATCAAGCAACAAGCTGTACAGCTTGAGCAGGCGAATc                                 >  1:1600107/1‑69 (MQ=255)
                         aGGAGAGCCAAAAAGCCGAGCTGGAAGGCATTATCAAGCAACAAGCTGTACAGCTTGAGCAGGCGAATc                                 >  1:597304/1‑69 (MQ=255)
                         aGGAGAGCCAAAAAGCCGAGCTGGAAGGCATTATCAAGCAACAAGCTGTACAGCTTGAGCAGGCGAATc                                 >  1:635803/1‑69 (MQ=255)
                         aGGAGAGCCAAAAAGCCGAGCTGGAAGGCATTATCAAGCAACAAGCTGTACAGCTTGAGCAGGCGAATc                                 >  1:724389/1‑69 (MQ=255)
                         aGGAGAGCCAAAAAGCCGAGCTGGAAGGCATTATCAAGCAACAAGCTGTACAGCTTGAGCAGGCGAATc                                 >  1:949525/1‑69 (MQ=255)
                         aGGAGAGCCAAAAAGCCGAGCTGGAAGGCATTATCAAGCAACAAGCTGTACAGCTTGAGCAGGCGAATc                                 >  1:959543/1‑69 (MQ=255)
                         aGGAGAGCCAAAAAGCCGAGCTGGAAGGCATTATCAAGCAACAAGCTGTACAGCTTGAGCAGGCGAATc                                 >  1:1010014/1‑69 (MQ=255)
                         aGGAGAGCCAAAAAGCCGAGCTGGAAGGCATTATCAAGCAACAAGCTGTACAGCTTGAGCAGGCGAATc                                 >  1:960290/1‑69 (MQ=255)
                                  aaaaaGCCGAGCTGGAAGGCATTATCAAGCAACAAGCTg                                                      <  1:2572546/39‑1 (MQ=255)
                                  aaaaaGCCGAGCTGGAAGGCATTATCAAGCAACAAGCTg                                                      <  1:3333954/39‑1 (MQ=255)
                                  aaaaaGCCGAGCTGGAAGGCATTATCAAGCAACAAGCTg                                                      <  1:469281/39‑1 (MQ=255)
                                  aaaaaGCCGAGCTGGAAGGCATTATCAAGCAACAAGCTg                                                      <  1:673054/39‑1 (MQ=255)
                                  aaaaaGCCGAGCTGGAAGGCATTATCAAGCAACAAGCTg                                                      <  1:735612/39‑1 (MQ=255)
                                  aaaaaGCCGAGCTGGAAGGCATTATCAAGCAACAAGCTg                                                      <  1:2631627/39‑1 (MQ=255)
                                  aaaaaGCCGAGCTGGAAGGCATTATCAAGCAACAAGCTg                                                      <  1:2280198/39‑1 (MQ=255)
                                  aaaaaGCCGAGCTGGAAGGCATTATCAAGCAACAAGCTg                                                      <  1:2208398/39‑1 (MQ=255)
                                  aaaaaGCCGAGCTGGAAGGCATTATCAAGCAACAAGCTg                                                      <  1:2244591/39‑1 (MQ=255)
                                  aaaaaGCCGAGCTGGAAGGCATTATCAAGCAACAAGCTg                                                      <  1:2248612/39‑1 (MQ=255)
                                  aaaaaGCCGAGCTGGAAGGCATTATCAAGCAACAAGCTg                                                      <  1:1333396/39‑1 (MQ=255)
                                  aaaaaGCCGAGCTGGAAGGCATTATCAAGCAACAAGCTg                                                      <  1:1298397/39‑1 (MQ=255)
                                  aaaaaGCCGAGCTGGAAGGCATTATCAAGCAACAAGCTg                                                      <  1:2440895/39‑1 (MQ=255)
                                  aaaaaGCCGAGCTGGAAGGCATTATCAAGCAACAAGCTg                                                      <  1:2523321/39‑1 (MQ=255)
                                   aaaaGCCGAGCTGGAAGGCATTATTAAGCAACAAGCTGCACAACTTAAGCAGGCGAATCGTCAGCAAGa                       <  1:2409758/69‑1 (MQ=255)
                                   aaaaGCCGAGCTGGAAGGCATTATCAAGCAACAAGCTg                                                      <  1:1264065/38‑1 (MQ=255)
                                   aaaaGCCGAGCTGGAAGGCATTATCAAGCAACAAGCTg                                                      <  1:1528571/38‑1 (MQ=255)
                                         cGAGCTGGAAGGCATTATTAAGCAACAAGCTGCACAACTTAAGCAGGCGAATCGTCAGCAAGAAACGCt                 <  1:789641/69‑1 (MQ=255)
                                                     cATTATTAAGCAACAAGCTGCACAACTTAAGCAGGCGAATCGTCAGCAAGAAACGCTGGCAAAACAg       >  1:3084629/1‑67 (MQ=255)
                                                     cATTATTAAGCAACAAGCTGCACAACTTAAGCAGGCGAATCGTCAGCAAGAAACGCTGGCAAAACAGt      >  1:3017792/1‑68 (MQ=255)
                                                     cATTATTAAGCAACAAGCTGCACAACTTAAGCAGGCGAATCGTCAGCAAGAAACGCTGGCAAAACAGt      >  1:395861/1‑68 (MQ=255)
                                                     cATTATTAAGCAACAAGCTGCACAACTTAAGCAGGCGAATCGTCAGCAAGAAACGCTGGCAAAACAGt      >  1:1390782/1‑68 (MQ=255)
                                                     cATTATTAAGCAACAAGCTGCACAACTTAAGCAGGCGAATCGTCAGCAAGAAACGCTGGCAAAACAGt      >  1:3348454/1‑68 (MQ=255)
                                                     cATTATTAAGCAACAAGCTGCACAACTTAAGCAGGCGAATCGTCAGCAAGAAACGCTGGCAAAACAGt      >  1:2215983/1‑68 (MQ=255)
                                                     cATTATTAAGCAACAAGCTGCACAACTTAAGCAGGCGAATCGTCAGCAAGAAACGCTGGCAAAACAGt      >  1:2277107/1‑68 (MQ=255)
                                                     cATTATTAAGCAACAAGCTGCACAACTTAAGCAGGCGAATCGTCAGCAAGAAACGCTGGCAAAACAGt      >  1:2725478/1‑68 (MQ=255)
                                                     cATTATTAAGCAACAAGCTGCACAACTTAAGAAGGCGAATCGTCAGCAAGAAACGCTGGCAAAACAg       >  1:3343150/1‑67 (MQ=255)
                                                        tattaAGCAACAAGCTGCACAACTTAAGCAGGCGAATCGTCAGCAAGAAACGCTGGCAAAACAGTTgg   >  1:1008962/1‑68 (MQ=255)
                                                        tattaAGCAACAAGCTGCACAACTTAAGCAGGCGAATCGTCAGCAAGAAACGCTGGCAAAACAGTTgg   >  1:529616/1‑68 (MQ=255)
                                                        tattaAGCAACAAGCTGCACAACTTAAGCAGGCGAATCGTCAGCAAGAAACGCTGGCAAAACAGTTgg   >  1:1755494/1‑68 (MQ=255)
                                                        tattaAGCAACAAGCTGCACAACTTAAGCAGGCGAATCGTCAGCAAGAAACGCTGGCAAAACAGTTgg   >  1:1091266/1‑68 (MQ=255)
                                                        tattaAGCAACAAGCTGCACAACTTAAGCAGGCGAATCGTCAGCAAGAAACGCTGGCAAAACAGTTgg   >  1:3329609/1‑68 (MQ=255)
                                                        tattaAGCAACAAGCTGCACAACTTAAGCAGGCGAATCGTCAGCAAGAAACGCTGGCAAAACAGTTgg   >  1:3000434/1‑68 (MQ=255)
                                                        tattaAGCAACAAGCTGCACAACTTAAGCAGGCGAATCGTCAGCAAGAAACGCTGGCAAAACAGTTgg   >  1:2760613/1‑68 (MQ=255)
                                                         attaAGCAACAAGCTGCACAACTTAAGCAGGCGAATCGTCAGCAAGAAACGCTGGCAAAACAGTTGGa  >  1:371102/1‑68 (MQ=255)
                                                         attaAGCAACAAGCTGCACAACTTAAGCAGGCGAATCGTCAGCAAGAAACGCTGGCAAAACAGTTGGa  >  1:2003500/1‑68 (MQ=255)
                                                         attaAGCAACAAGCTGCACAACTTAAGCAGGCGAATCGTCAGCAAGAAACGCTGGCAAAACAGTTGGa  >  1:3316920/1‑68 (MQ=255)
                                                         attaAGCAACAAGCTGCACAACTTAAGCAGGCGAATCGTCAGCAAGAAACGCTGGCAAAACAGTTGGa  >  1:1568249/1‑68 (MQ=255)
                                                         attaAGCAACAAGCTGCACAACTTAAGCAGGCGAATCGTCAGCAAGAAACGCTGGCAAAACAGTTGGa  >  1:2094456/1‑68 (MQ=255)
                                                         attaAGCAACAAGCTGCACAACTTAAGCAGGCGAATCGTCAGCAAGAAACGCTGGCAAAACAGTTGGa  >  1:148273/1‑68 (MQ=255)
                                                          ttaAGCAACAAGCTGCACAACTTAAGCAGGCGAATCGTCAGCAAGAAACGCTGGCAAAACAGTTGGa  >  1:2557061/1‑67 (MQ=255)
                                                          ttaAGCAACAAGCTGCACAACTTAAGCAGGCGAATCGTCAGCAAGAAACGCTGGCAAAACAGTTGGa  >  1:1877960/1‑67 (MQ=255)
                                                          ttaAGCAACAAGCTGCACAACTTAAGCAGGCGAATCGTCAGCAAGAAACGCTGGCAAAACAGTTGGa  >  1:2748080/1‑67 (MQ=255)
                                                          ttaAGCAACAAGCTGCACAACTTAAGCAGGCGAATCGTCAGCAAGAAACGCTGGCAAAACAGTTGGa  >  1:1121755/1‑67 (MQ=255)
                                                          ttaAGCAACAAGCTGCACAACTTAAGCAGGCGAATCGTCAGCAAGAAACGCTGGCAAAACAGTTGGa  >  1:840506/1‑67 (MQ=255)
                                                          ttaAGCAACAAGCTGCACAACTTAAGCAGGCGAATCGTCAGCAAGAAACGCTGGCAAAACAGTTGGa  >  1:2750629/1‑67 (MQ=255)
                                                          ttaAGCAACAAGCTGCACAACTTAAGCAGGCGAATCGTCAGCAAGAAACGCTGGCAAAACAGTTGGa  >  1:2870286/1‑67 (MQ=255)
                                                          ttaAGCAACAAGCTGCACAACTTAAGCAGGCGAATCGTCAGCAAGAAACGCTGGCAAAACAGTTGGa  >  1:3231798/1‑67 (MQ=255)
                                                           |                                                                 
CAACTGACGGCATTGCAAAAAGCCCAGGAGAGCCAAAAAGCCGAGCTGGAAGGCATTATTAAGCAACAAGCTGCACAACTTAAGCAGGCGAATCGTCAGCAAGAAACGCTGGCAAAACAGTTGGA  >  minE/2409769‑2409893

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A