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 306,979 C→T 44.9% S36S (TCG→TCA)  ylaB ← conserved inner membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE306,9790CT44.9% 26.1 / 89.7 112S36S (TCG→TCA) ylaBconserved inner membrane protein
Reads supporting (aligned to +/- strand):  ref base C (51/10);  new base T (22/28);  total (74/38)
Fisher's exact test for biased strand distribution p-value = 1.76e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 113 total aligned reads displayed.

GCCACCTTATTGGCTCGAATAGCGACGCGGGAGGAATAGGTATCCAGCTCTTCAATAAACGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGA  >  minE/306920‑307042
                                                           |                                                               
gCCACCTTATTGGCTCGAATAGCGACGCGGGAGGAATAGGTATCCAGCTCTTCAATAAACGATGTTTCt                                                        <  1:1975689/69‑1 (MQ=255)
gCCACCTTATTGGCTCGAATAGCGACGCGGGAGGAATAGGTATCCAGCTCTTCAATAAACGATGTTTCt                                                        <  1:1412307/69‑1 (MQ=255)
gCCACCTTATTGGCTCGAATAGCGACGCGGGAGGAATAGGTATCCAGCTCTTCAATAAACGATGTTTCt                                                        <  1:134379/69‑1 (MQ=255)
       tATTGGCTCGAATAGCGACGCGGGAGGAATAGGTATCCAGCTCTTCAATAAACGATGTTTCTACctgct                                                 <  1:1655590/69‑1 (MQ=255)
           ggCTCGAATAGCGACGCGGGAGGAATAGGTATCCAGCTCTTCAATAAAc                                                                 >  1:1874840/1‑49 (MQ=255)
           ggCTCGAATAGCGACGCGGGAGGAATAGGTATCCAGCTCTTCAATAAACGATGTTTCTACCTGCTGATg                                             >  1:1856114/1‑69 (MQ=255)
           ggCTCGAATAGCGACGCGGGAGGAATAGGTATCCAGCTCTTCAATAAACGATGTTTCTACCTGCTGATg                                             >  1:1450650/1‑69 (MQ=255)
           ggCTCGAATAGCGACGCGGGAGGAATAGGTATCCAGCTCTTCAATAAACGATGTTTCTACCTGCTGATg                                             >  1:1319121/1‑69 (MQ=255)
           ggCTCGAATAGCGACGCGGGAGGAATAGGTATCCAGCTCTTCAATAAACGATGTTTCTACCTGCTGATg                                             >  1:1268020/1‑69 (MQ=255)
           ggCTCGAATAGCGACGCGGGAGGAATAGGTATCCAGCTCTTCAATAAACGATGTTTCTACCTGCTGATg                                             >  1:3181608/1‑69 (MQ=255)
           ggCTCGAATAGCGACGCGGGAGGAATAGGTATCCAGCTCTTCAATAAACGATGTTTCTACCTGCTGATg                                             >  1:2825157/1‑69 (MQ=255)
           ggCTCGAATAGCGACGCGGGAGGAATAGGTATCCAGCTCTTCAATAAACGATGTTTCTACCTGCTGATg                                             >  1:1169488/1‑69 (MQ=255)
           ggCTCGAATAGCGACGCGGGAGGAATAGGTATCCAGCTCTTCAATAAACGATGTTTCTACCTGCTGATg                                             >  1:1125658/1‑69 (MQ=255)
                  aTAGCGACGCGGGAGGAATAGGTATCCAGCTCTTCAATAAACGATGTTTCTACCTGCTGATGGgcca                                        >  1:3145580/1‑67 (MQ=255)
                  aTAGCGACGCGGGAGGAATAGGTATCCAGCTCTTCAATAAACGATGTTTCTACCTGCTGATGGgcca                                        >  1:3060428/1‑67 (MQ=255)
                   tAGCGACGCGGGAGGAATACGTATTCAGCTCTTCAATAAATGATGtt                                                           >  1:1108513/1‑47 (MQ=255)
                   tAGCGACGCGGGAGGAATACGTATTCAGCTCTTCAATAAATGATGTTTCTa                                                       >  1:2776064/1‑51 (MQ=255)
                   tAGCGACGCGGGAGGAATACGTATTCAGCTCTTCAATAAATGATGTTTCTACctgct                                                 >  1:2626319/1‑57 (MQ=255)
                   tAGCGACGCGGGAGGAATACGTATTCAGCTCTTCAATAAATGATGTTTCTACctgct                                                 >  1:3075793/1‑57 (MQ=255)
                   tAGCGACGCGGGAGGAATACGTATTCAGCTCTTCAATAAATGATGTTTCTACctgct                                                 >  1:1962218/1‑57 (MQ=255)
                   tAGCGACGCGGGAGGAATACGTATTCAGCTCTTCAATAAATGATGTTTCTACctgct                                                 >  1:3126207/1‑57 (MQ=255)
                   tAGCGACGCGGGAGGAATACGTATTCAGCTCTTCAATAAATGATGTTTCTACctgct                                                 >  1:425435/1‑57 (MQ=255)
                   tAGCGACGCGGGAGGAATACGTATTCAGCTCTTCAATAAATGATGTTTCTACctgct                                                 >  1:1557534/1‑57 (MQ=255)
                   tAGCGACGCGGGAGGAATACGTATTCAGCTCTTCAATAAATGATGTTTCTACctgct                                                 >  1:220862/1‑57 (MQ=255)
                   tAGCGACGCGGGAGGAATACGTATTCAGCTCTTCAATAAATGATGTTTCTACctgct                                                 >  1:2436536/1‑57 (MQ=255)
                   tAGCGACGCGGGAGGAATACGTATTCAGCTCTTCAATAAATGATGTTTCTACctgct                                                 >  1:331342/1‑57 (MQ=255)
                   tAGCGACGCGGGAGGAATACGTATTCAGCTCTTCAATAAATGATGTTTCTACctgct                                                 >  1:282594/1‑57 (MQ=255)
                   tAGCGACGCGGGAGGAATACGTATTCAGCTCTTCAATAAATGATGTTTCTACctgct                                                 >  1:1394978/1‑57 (MQ=255)
                   tAGCGACGCGGGAGGAATACGTATTCAGCTCTTCAATAAATGATGTTTCTACctgct                                                 >  1:137626/1‑57 (MQ=255)
                   tAGCGACGCGGGAGGAATACGTATTCAGCTCTTCAATAAATGATGTTTCTACctgct                                                 >  1:1136801/1‑57 (MQ=255)
                   tAGCGACGCGGGAGGAATACGTATTCAGCTCTTCAATAAATGATGTTTCTACctgct                                                 >  1:273325/1‑57 (MQ=255)
                   tAGCGACGCGGGAGGAATACGTATTCAGCTCTTCAATAAATGATGTTTCTACctgc                                                  >  1:3132442/1‑56 (MQ=255)
                   tAGCGACGCGGGAGGAATACGGATTCAGCTCTTCAATAAATGATGTTTCTACctgct                                                 >  1:452503/1‑57 (MQ=255)
                   tAGCGACCCGGGAGGAATACGTATTCAGCTCTTCAATAAATGATGTTTCTACctgct                                                 >  1:3263567/1‑57 (MQ=255)
                             ggaggaATAGGTATCCAGCTCTTCAATAAACGATGTTTCt                                                        <  1:1026369/40‑1 (MQ=255)
                                      ggTATCCAGCTCTTCAATAAACGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACa                    >  1:536000/1‑67 (MQ=255)
                                      ggTATCCAGCTCTTCAATAAACGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACa                    >  1:1714031/1‑67 (MQ=255)
                                      ggTATCCAGCTCTTCAATAAACGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACa                    >  1:3397633/1‑67 (MQ=255)
                                      ggTATCCAGCTCTTCAATAAACGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACa                    >  1:2419611/1‑67 (MQ=255)
                                      cgTATCCAGCTCTTCAATAAAAGATGTTTCTACATGCTGATGGGCCAGCCAGATGCTTAAGc                         >  1:1508340/2‑62 (MQ=255)
                                            cAGCTCTTCAATAAACGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACAGTCAGCaa            <  1:4931/69‑1 (MQ=255)
                                            cAGCTCTTCAATAAACGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACAGGCAGCaa            >  1:422630/1‑69 (MQ=255)
                                            cAGCTCTTCAATAAACGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACAGGCAGCaa            <  1:1176115/69‑1 (MQ=255)
                                            cAGCTCTTCAATAAACGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACAGGCAGCaa            >  1:1177995/1‑69 (MQ=255)
                                            cAGCTCTTCAATAAACGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACAGGCAGCaa            >  1:1206465/1‑69 (MQ=255)
                                            cAGCTCTTCAATAAACGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACAGGCAGCaa            >  1:1209566/1‑69 (MQ=255)
                                            cAGCTCTTCAATAAACGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACAGGCAGCaa            >  1:1817579/1‑69 (MQ=255)
                                            cAGCTCTTCAATAAACGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACAGGCAGCaa            >  1:424092/1‑69 (MQ=255)
                                              gCTCTTCAATAAACGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACAGGCAGCAATa          <  1:1532654/69‑1 (MQ=255)
                                              gCTCTTCAATAAACGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACAGGCAGCAATa          <  1:174803/69‑1 (MQ=255)
                                                 ctTCAATAAATGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTg       <  1:1090493/69‑1 (MQ=255)
                                                 ctTCAATAAATGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTg       <  1:890284/69‑1 (MQ=255)
                                                 ctTCAATAAATGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTg       <  1:2999875/69‑1 (MQ=255)
                                                 ctTCAATAAATGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTg       <  1:2993093/69‑1 (MQ=255)
                                                 ctTCAATAAATGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTg       <  1:288072/69‑1 (MQ=255)
                                                 ctTCAATAAATGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTg       <  1:1180441/69‑1 (MQ=255)
                                                 ctTCAATAAATGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTg       <  1:3059188/69‑1 (MQ=255)
                                                 ctTCAATAAATGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTg       <  1:2731575/69‑1 (MQ=255)
                                                 ctTCAATAAATGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTg       <  1:2348080/69‑1 (MQ=255)
                                                 ctTCAATAAATGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTg       <  1:355944/69‑1 (MQ=255)
                                                 ctTCAATAAATGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTg       <  1:3418372/69‑1 (MQ=255)
                                                 ctTCAATAAATGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTg       <  1:2245543/69‑1 (MQ=255)
                                                 ctTCAATAAATGAAGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTg       <  1:1053887/69‑1 (MQ=255)
                                                  ttCAATAAATGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTg       <  1:196099/68‑1 (MQ=255)
                                                  ttCAATAAATGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTg       <  1:2619669/68‑1 (MQ=255)
                                                  ttCAATAAATGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTg       <  1:471502/68‑1 (MQ=255)
                                                    cAATAAACGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGaa     >  1:976085/1‑68 (MQ=255)
                                                    cAATAAACGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGaa     >  1:360600/1‑68 (MQ=255)
                                                    cAATAAACGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGaa     >  1:527861/1‑68 (MQ=255)
                                                    cAATAAACGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGaa     >  1:357580/1‑68 (MQ=255)
                                                    cAATAAACGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGaa     >  1:1359793/1‑68 (MQ=255)
                                                    cAATAAACGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGaa     >  1:1523052/1‑68 (MQ=255)
                                                    cAATAAACGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGaa     >  1:1575495/1‑68 (MQ=255)
                                                    cAATAAACGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGaa     >  1:278059/1‑68 (MQ=255)
                                                    cAATAAACGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGaa     >  1:1751408/1‑68 (MQ=255)
                                                    cAATAAACGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGaa     >  1:2624757/1‑68 (MQ=255)
                                                    cAATAAACGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGaa     >  1:1775240/1‑68 (MQ=255)
                                                    cAATAAACGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGaa     >  1:2012464/1‑68 (MQ=255)
                                                    cAATAAACGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGa      >  1:319495/1‑67 (MQ=255)
                                                    cAATAAACGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGa      >  1:1921927/1‑67 (MQ=255)
                                                       tAAATGATGTTTCTTCCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGa  <  1:1005540/68‑1 (MQ=255)
                                                       tAAATGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGa  <  1:3424141/68‑1 (MQ=255)
                                                       tAAATGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGa  <  1:938955/68‑1 (MQ=255)
                                                       tAAATGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGa  <  1:3407306/68‑1 (MQ=255)
                                                       tAAATGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGa  <  1:2552089/68‑1 (MQ=255)
                                                       tAAATGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGa  <  1:928815/68‑1 (MQ=255)
                                                       tAAATGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGa  <  1:724894/68‑1 (MQ=255)
                                                       tAAATGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGa  <  1:1541821/68‑1 (MQ=255)
                                                       tAAATGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGa  <  1:3014733/68‑1 (MQ=255)
                                                       tAAATGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGa  <  1:3027938/68‑1 (MQ=255)
                                                       tAAATGATGTTTCTACCTGCCGATGGGCCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGa  <  1:1122680/68‑1 (MQ=255)
                                                       tAAACGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAgac                        >  1:2021875/1‑44 (MQ=255)
                                                       tAAACGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGcc                        >  1:1295599/1‑46 (MQ=255)
                                                       tAAACGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGcc                        >  1:2921259/1‑46 (MQ=255)
                                                       tAAACGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGcc                        >  1:164033/1‑46 (MQ=255)
                                                       tAAACGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGcc                        >  1:2712028/1‑46 (MQ=255)
                                                       tAAACGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGcc                        >  1:2539493/1‑46 (MQ=255)
                                                       tAAACGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGcc                        >  1:963341/1‑46 (MQ=255)
                                                       tAAACGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGcc                        >  1:967280/1‑46 (MQ=255)
                                                       tAAACGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGcc                        >  1:3066994/1‑46 (MQ=255)
                                                           |                                                               
GCCACCTTATTGGCTCGAATAGCGACGCGGGAGGAATAGGTATCCAGCTCTTCAATAAACGATGTTTCTACCTGCTGATGGGCCAGCCAGATGCTTAAGCCGACAGGCAGCAATACTGAAAGA  >  minE/306920‑307042

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