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
A1 F3 I0 R2 260 44.3 3360226 90.5% 3041004 64.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 1,477,935 G→A 32.4% E360K (GAA→AAA)  ydbD → hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb1,477,9350GA32.4% 94.5 / 61.6 74E360K (GAA→AAA) ydbDhypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (26/24);  new base A (16/8);  total (42/32)
Fisher's exact test for biased strand distribution p-value = 3.17e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGTCGAAATAATGACGCGAATGAGTCGTCTACCTGATGGTGTCGGTCCGTTGAATCTTGCGCTACGTGAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGAAAAGAGATTGGGATATGATCA  >  W3110S.gb/1477868‑1477992
                                                                   |                                                         
tGTCGAAATAATGACGCGAATGAGTCGTCTACCTGATGGTGTCGGTCCGTTGAATCTTGCGCTACGTaaa                                                         >  1:1519150/1‑70 (MQ=255)
tGTCGAAATAATGACGCGAATGAGTCGTCTACCTGATGGTGTCGGTCCGTTGAATCTTGCGCTACGTaaa                                                         >  1:1773199/1‑70 (MQ=255)
tGTCGAAATAATGACGCGAATGAGTCGTCTACCTGATGGTGTCGGTCCGTTGAATCTTGCGCTACGTaaa                                                         >  1:3081563/1‑70 (MQ=255)
tGTCGAAATAATGACGCGAATGAGTCGTCTACCTGATGGTGTCGGTCCGTTGAATCTTGCGCTACGTaaa                                                         >  1:2127140/1‑70 (MQ=255)
tGTCGAAATAATGACGCGAATGAGTCGTCTACCTGATGGTGTCGGTCCGTTGAATCTTGCGCTACGTaaa                                                         >  1:2083927/1‑70 (MQ=255)
tGTCGAAATAATGACGCGAATGAGTCGTCTACCTGATGGTGTCGGTCCGTTGAATCATGCGCTACGTaaa                                                         >  1:2475876/1‑70 (MQ=255)
  tCGAAATAATGACGCGAATGAGTCGTCTACCTGATGGTGTCGGTCCGTTGAATCTTGCGCTACGTaaa                                                         <  1:37194/68‑1 (MQ=255)
  tCGAAATAATGACGCGAATGAGTCGTCTACCTGATGGTGTCGGTCCGTTGAATCTTGCGCTACGTaaa                                                         <  1:1600543/68‑1 (MQ=255)
  tCGAAATAATGACGCGAATGAGTCGTCTACCTGATGGTGTCGGTCCGTTGAATCTTGCGCTACGTaaa                                                         <  1:289083/68‑1 (MQ=255)
  tCGAAATAATGACGCGAATGAGTCGTCTACCTGATGGTGTCGGTCCGTTGAATCTTGCGCTACGTaaa                                                         <  1:3315967/68‑1 (MQ=255)
  tCGAAATAATGACGCGAATGAGTCGTCTACCTGATGGTGTCGGTCCGTTGAATCTTGCGCTACGTaaa                                                         <  1:1287460/68‑1 (MQ=255)
  tCGAAATAATGACGCGAATGAGTCGTCTACCTGATGGTGTCGGTCCGTTGAATCTTGCGCTACGTaaa                                                         <  1:1272643/68‑1 (MQ=255)
  tCGAAATAATGACGCGAATGAGTCGTCTACCTGATGGTGTCGGTCCGTTGAATCTTGCGCTACGTaaa                                                         <  1:1153344/68‑1 (MQ=255)
  tCGAAATAATGACGCGAATGAGTCGTCTACCTGATGGTGTCGGTCCGTTGAATCTTGCGCTACGTaaa                                                         <  1:1012131/68‑1 (MQ=255)
       ataatGACGCGAATGAGTCGTCTACCTGATGGTGTCGGTCCGTTGAATCTTGCGCTACGTAAAAAtct                                                    >  1:396086/1‑68 (MQ=255)
       ataatGACGCGAATGAGTCGTCTACCTGATGGTGTCGGTCCGTTGAATCTTGCGCTACGTAAAAATCTcc                                                  >  1:3314647/1‑70 (MQ=255)
                   aTGAGTCGTCTAGCTGATGGTGTCGGTCCGTTGAATCTTGCGCTACGTGAAAATCTCCCTCTGGATATCGt                                     <  1:293446/71‑1 (MQ=255)
                   aTGAGTCGTCTACCTGATGGTTTCGGTCCGTTGAATCTTGCGCTACGTGAAAATCTCCCTCTGGATATCGt                                     <  1:1600350/71‑1 (MQ=255)
                   aTGAGTCGTCTACCTGATGGTGTCGGTCCGTTGAATCTTGCGCTACGTGAAAATCTCCCTCTGGATATCGt                                     <  1:2562582/71‑1 (MQ=255)
                   aTGAGTCGTCTACCTGATGGTGTCGGTCCGTTGAATCTTGCGCTACGTGAAAATCTCCCTCTGGATATCGt                                     <  1:972110/71‑1 (MQ=255)
                   aTGAGTCGTCTACCTGATGGTGTCGGTCCGTTGAATCTTGCGCTACGTGAAAATCTCCCTCTGGATATCGt                                     <  1:2151782/71‑1 (MQ=255)
                   aTGAGTCGTCTACCTGATGGTGTCGGTCCGTTGAATCTTGCGCTACGTGAAAATCTCCCTCTGGATATCGt                                     <  1:1676182/71‑1 (MQ=255)
                   aTGAGTCGTCTACCTGATGGTGTCGGTCCGTTGAATCTTGCGCTACGTGAAAATCTCCCTCTGGATATCGt                                     <  1:2220941/71‑1 (MQ=255)
                          gtcTACCTGATGGTGTCGGTCCGTTGAATCTTGCGCTACGTGAAAATCTCCCTCTGGATATCGt                                     <  1:3047353/64‑1 (MQ=255)
                               ccTGATGGTGTCGGTCCGTTGAATCTTGCGCTACGTGAAAATCTCCCTCTGGATATCGTCATGACTCTgg                          >  1:1849673/1‑70 (MQ=255)
                               ccTGATGGTGTCGGTCCGTTGAATCTTGCGCTACGTGAAAATCTCCCTCTGGATATCGTCATGACTCTgg                          >  1:1292170/1‑70 (MQ=255)
                               ccTGATGGTGTCGGTCCGTTGAATCTTGCGCTACGTGAAAATCTCCCTCTGGATATCGTCATGACTCTGGc                         >  1:3035067/1‑71 (MQ=255)
                               ccTGATGGTGTCGGTCCGTTGAATCTTGCGCTACGTGAAAATCTCCCTCTGGATATCGTCATGACTCTGGc                         >  1:2002531/1‑71 (MQ=255)
                               ccTGATGGTGTCGGTCCGTTGAATCTTGCGCTACGTGAAAATCTCCCTCTGGATATCGTCATGACTCTGGc                         >  1:2996285/1‑71 (MQ=255)
                                  gATGGTGTCGGTCCGTTGAATCTTGCGCTACGTGAAAATCTCCCTCTGGATATCGTCATGACTCTGGCg                        >  1:172145/1‑69 (MQ=255)
                                  gATGGTGTCGGTCCGTTGAATCTTGCGCTACGTGAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGa                       >  1:1467982/1‑70 (MQ=255)
                                  gATGGTGTCGGTCCGTTGAATCTTGCGCTACGTGAAAATCTCCCTCTGGATATCGTAATGACTCTGGCGa                       >  1:2482531/1‑70 (MQ=255)
                                  gATGGTGTCGGTCCGTTGAATCTTGCGCTACGTAAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGa                       >  1:1192359/1‑70 (MQ=255)
                                     ggTGTCGGTCCGTTGAATCTTGCGCTACGTGAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGaa                      >  1:3261315/1‑68 (MQ=255)
                                     ggTGTCGGTCCGTTGAATCTTGCGCTACGTGAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGaa                      >  1:593934/1‑68 (MQ=255)
                                     ggTGTCGGTCCGTTGAATCTTGCGCTACGTGAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGaa                      >  1:1071790/1‑68 (MQ=255)
                                        gtCGGTTCGTTGAATCTTGCGCTACGTAAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGaaaa                    >  1:2013824/1‑67 (MQ=255)
                                        gtCGGTCCGTTGAATCTTGCGCTACGTAAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGaaaa                    >  1:2470785/1‑67 (MQ=255)
                                        gtCGGTCCGTTGAATCTTGCGCTACGTAAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGaaaa                    >  1:917002/1‑67 (MQ=255)
                                        gtCGGTCCGTTGAATCTTGCGCTACGTAAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGaaaa                    >  1:2840896/1‑67 (MQ=255)
                                              ccGTTGAATCTTGCGCTACGTAAAAATCTCCCTCTGGATATCGTCATGACTCTGTCGAAAAGAGATTGGGa          >  1:2945015/1‑71 (MQ=255)
                                              ccGTTGAATCTTGCGCTACGTAAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGAAAAGAGATTGGGa          >  1:3329602/1‑71 (MQ=255)
                                              ccGTTGAATCTTGCGCTACGTAAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGAAAAGAGATTGGGa          >  1:1116603/1‑71 (MQ=255)
                                               cGTTGAATCTTGCGCTACGTAAAAATCTCCCTCTGGATATCGTCATGAc                               >  1:418455/1‑49 (MQ=255)
                                               cGTTGAATCTTGCGCTACGTAAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGAAAAGAGATTGGGa          >  1:41139/1‑70 (MQ=255)
                                               cGTTGAATCTTGCGCTACGTAAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGAAAAGAGATTGGGa          >  1:549366/1‑70 (MQ=255)
                                               cGTTGAATCTTGCGCTACGTAAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGAAAAGAGATTGGGa          >  1:541071/1‑70 (MQ=255)
                                               cGTTGAATCTTGCGCTACGTAAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGAAAAGAGATTGGGa          >  1:1567759/1‑70 (MQ=255)
                                               cGTTGAATCTTGCGCTACGTAAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGAAAAGAGATTGGGa          >  1:441288/1‑70 (MQ=255)
                                                   gAATCTTGCGCTACGTAAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGAAAAGAGATTGGGATATg      <  1:1548236/70‑1 (MQ=255)
                                                   gAATCTTGCGCTACGTAAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGAAAAGAGATTGGGATATg      <  1:36094/70‑1 (MQ=255)
                                                   gAATCTTGCGCTACGTAAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGAAAAGAGATTGGGATATg      <  1:2870550/70‑1 (MQ=255)
                                                   gAATCTTGCGCTACGTAAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGAAAAGAGATTGGGATATg      <  1:2120793/70‑1 (MQ=255)
                                                   gAATCTTGCGCTACGTAAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGAAAAGAGATTGGGATATg      <  1:669923/70‑1 (MQ=255)
                                                   gAATCTTGCGCTACGTAAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGAAAAGAGATTGGGATATg      <  1:1380759/70‑1 (MQ=255)
                                                   gAATCTTGCGCTACGTAAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGAAAAGAGATTGGGATATg      <  1:2305584/70‑1 (MQ=255)
                                                   gAATCTTGCGCTACGTAAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGAAAAGAGATTGGGATATg      <  1:2164672/70‑1 (MQ=255)
                                                      tCTTGCGCTACGTGAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGAAAAGAGATTGGGATATGAt    >  1:3315688/1‑69 (MQ=255)
                                                      tCTTGCGCTACGTGAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGAAAAGAGATTGGGATATGATCa  >  1:3305922/1‑71 (MQ=255)
                                                      tCTTGCGCTACGTGAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGAAAAGAGATTGGGATATGATCa  >  1:3302003/1‑71 (MQ=255)
                                                      tCTTGCGCTACGTGAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGAAAAGAGATTGGGATATGATCa  >  1:439564/1‑71 (MQ=255)
                                                      tCTTGCGCTACGTGAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGAAAAGAGATTGGGATATGATCa  >  1:448029/1‑71 (MQ=255)
                                                      tCTTGCGCTACGTGAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGAAAAGAGATTGGGATATGATCa  >  1:1094663/1‑71 (MQ=255)
                                                      tCTTGCGCTACGTGAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGAAAAGAGATTGGGATATGATCa  >  1:738921/1‑71 (MQ=255)
                                                      tCTTGCGCTACGTGAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGAAAAGAGATTGGGATATGATCa  >  1:76340/1‑71 (MQ=255)
                                                      tCTTGCGCTACGTGAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGAAAAGAGATTGGGATATGATCa  >  1:1448435/1‑71 (MQ=255)
                                                      tCTTGCGCTACGTGAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGAAAAGAGATTGGGATATGATCa  >  1:2942720/1‑71 (MQ=255)
                                                      tCTTGCGCTACGTGAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGAAAAGAGATTGGGATATGATCa  >  1:2253502/1‑71 (MQ=255)
                                                      tCTTGCGCTACGTGAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGAAAAGAGATTGGGATATGATCa  >  1:2461040/1‑71 (MQ=255)
                                                      tCTTGCGCTACGTGAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGAAAAGAGATTGGGATATGATCa  >  1:284435/1‑71 (MQ=255)
                                                      tCTTGCGCTACGTGAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGAAAAGAGATTGGGATATGATCa  >  1:2629866/1‑71 (MQ=255)
                                                      tCTTGCGCTACGTGAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGAAAAGAGATTAGGATATGATCa  >  1:1481437/1‑71 (MQ=255)
                                                                  tGAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGAAAAGAGATTGGGATATGATCa  <  1:2782701/59‑1 (MQ=255)
                                                                  tGAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGAAAAGAGATTGGGATATGATCa  <  1:1035393/59‑1 (MQ=255)
                                                                  tGAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGAAAAGAGATTGGGATATGATCa  <  1:1065295/59‑1 (MQ=255)
                                                                  tGAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGAAAAGAGATTGGGATATGATCa  <  1:605271/59‑1 (MQ=255)
                                                                  tGAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGAAAAGAGATTGGGATATGATCa  <  1:2136728/59‑1 (MQ=255)
                                                                  tGAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGAAAAGAGATTGGGATATGATCa  <  1:542708/59‑1 (MQ=255)
                                                                  tGAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGAAAAGAGATTGGGATATGATCa  <  1:529453/59‑1 (MQ=255)
                                                                  tGAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGAAAAGAGATTGGGATATGATCa  <  1:2757826/59‑1 (MQ=255)
                                                                  tGAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGAAAAGAGATTGGGATATGATCa  <  1:2172162/59‑1 (MQ=255)
                                                                  tGAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGAAAAGAGATTGGGATATGATCa  <  1:2017243/59‑1 (MQ=255)
                                                                  tGAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGAAAAGAGATTGGGATATGATCa  <  1:1860389/59‑1 (MQ=255)
                                                                  tGAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGAAAAGAGATTGGGATATGATCa  <  1:1360195/59‑1 (MQ=255)
                                                                  tGAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGAAAAGAGATTGGGATATGATCa  <  1:1695339/59‑1 (MQ=255)
                                                                  tGAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGAAAAGAGATTGGGATATGATCa  <  1:1377535/59‑1 (MQ=255)
                                                                  tGAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGAAAAGAGATTGGGATATGATCa  <  1:1385629/59‑1 (MQ=255)
                                                                  tGAAAATCTCCCTCTGGATATCGTAATGACTCTGGCGAAAAGAGATTGGGATATGATCa  <  1:20931/59‑1 (MQ=255)
                                                                   gAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGAAAAGAGATTGGGATATGATCa  <  1:2797233/58‑1 (MQ=255)
                                                                   gAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGAAAAGAGATTGGGATATGATCa  <  1:2155009/58‑1 (MQ=255)
                                                                   |                                                         
TGTCGAAATAATGACGCGAATGAGTCGTCTACCTGATGGTGTCGGTCCGTTGAATCTTGCGCTACGTGAAAATCTCCCTCTGGATATCGTCATGACTCTGGCGAAAAGAGATTGGGATATGATCA  >  W3110S.gb/1477868‑1477992

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