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 2,508,088 C→A 17.1% G615V (GGC→GTC)  ypdD ← fused predicted PTS enzymes Hpr component, enzyme I component, and enzyme IIA component

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,508,0880CA17.1% 348.4 / 38.4 121G615V (GGC→GTC) ypdDfused predicted PTS enzymes Hpr component, enzyme I component, and enzyme IIA component
Reads supporting (aligned to +/- strand):  ref base C (24/76);  new base A (4/17);  total (28/93)
Fisher's exact test for biased strand distribution p-value = 7.80e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 123 total aligned reads displayed.

ACTCATACTCAGCTCATCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGTAACTATTTGCTGCAA  >  W3110S.gb/2508027‑2508152
                                                             |                                                                
actcatactcaGCTCATCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCa                                                          >  1:2747362/1‑70 (MQ=255)
actcatactcaGCTCATCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCa                                                          >  1:2144684/1‑70 (MQ=255)
   catactcaGCTCATCCAGGCCCAGCCCAAGCAGTAGCTGCAGATAACGGCTTTCACCGCCCAGTTCAcc                                                        >  1:1570243/1‑69 (MQ=255)
   catactcaGCTCATCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCAcc                                                        >  1:2649249/1‑69 (MQ=255)
   catactcaGCTCATCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCAcc                                                        >  1:2824943/1‑69 (MQ=255)
   catactcaGCTCATCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCAcc                                                        >  1:2825963/1‑69 (MQ=255)
   catactcaGCTCATCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCAcc                                                        >  1:2909395/1‑69 (MQ=255)
   catactcaGCTCATCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCAcc                                                        >  1:143154/1‑69 (MQ=255)
   catactcaGCTCATCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCAcc                                                        >  1:2684777/1‑69 (MQ=255)
   catactcaGCTCATCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCAcc                                                        >  1:199059/1‑69 (MQ=255)
   catactcaGCTCATCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCAcc                                                        >  1:1042245/1‑69 (MQ=255)
    atactcaGCTCATCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCGCCGccc                                                                >  1:673768/1‑60 (MQ=255)
    atactcaGCTCATCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCa                                                          >  1:2503670/1‑66 (MQ=255)
    atactcaGCTCATCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCa                                                          >  1:2096504/1‑66 (MQ=255)
    atactcaGCTCATCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCa                                                          >  1:1187129/1‑66 (MQ=255)
    atactcaGCTCATCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCa                                                          >  1:1404362/1‑66 (MQ=255)
    atactcaGCTCATCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCa                                                          >  1:21586/1‑66 (MQ=255)
    atactcaGCTCATCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCa                                                          >  1:188154/1‑66 (MQ=255)
    atactcaGCTCATCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCa                                                          >  1:157338/1‑66 (MQ=255)
    atactcaGCTCATCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCGCa                                                     <  1:1462626/71‑1 (MQ=255)
    atactcaGCTCATCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCGCa                                                     <  1:2438424/71‑1 (MQ=255)
    atactcaGCTCATCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCGCa                                                     <  1:1076396/71‑1 (MQ=255)
    atactcaGCTCATCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCGCa                                                     <  1:2296306/71‑1 (MQ=255)
               aTCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAg                                                              <  1:965477/51‑1 (MQ=255)
               aTCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAg                                                              <  1:1830791/51‑1 (MQ=255)
               aTCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAg                                                              <  1:2274050/51‑1 (MQ=255)
               aTCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAg                                                              <  1:1700611/51‑1 (MQ=255)
               aTCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAg                                                              <  1:1742915/51‑1 (MQ=255)
               aTCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAg                                                              <  1:3170466/51‑1 (MQ=255)
               aTCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAg                                                              <  1:830121/51‑1 (MQ=255)
               aTCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAg                                                              <  1:785138/51‑1 (MQ=255)
               aTCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAg                                                              <  1:738175/51‑1 (MQ=255)
               aTCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAg                                                              <  1:1217115/51‑1 (MQ=255)
               aTCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAg                                                              <  1:1229113/51‑1 (MQ=255)
                tCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGACCAg                                                              <  1:1011335/50‑1 (MQ=255)
                tCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGACCAg                                                              <  1:2473564/50‑1 (MQ=255)
                tCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGACCAg                                                              <  1:694279/50‑1 (MQ=255)
                tCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGACCAg                                                              <  1:2572299/50‑1 (MQ=255)
                tCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGACCAg                                                              <  1:632649/50‑1 (MQ=255)
                tCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGACCAg                                                              <  1:2595386/50‑1 (MQ=255)
                tCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGACCAg                                                              <  1:49556/50‑1 (MQ=255)
                tCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGACCAg                                                              <  1:333701/50‑1 (MQ=255)
                tCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGACCAg                                                              <  1:2915766/50‑1 (MQ=255)
                tCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGACCAg                                                              <  1:1002921/50‑1 (MQ=255)
                tCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGACCAg                                                              <  1:1262806/50‑1 (MQ=255)
                tCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGACCAg                                                              <  1:1909401/50‑1 (MQ=255)
                tCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGACCAg                                                              <  1:1960258/50‑1 (MQ=255)
                 ccAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGACCAg                                                              <  1:1510333/49‑1 (MQ=255)
                  cAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCAtt                                       <  1:2559216/71‑1 (MQ=255)
                  cAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGACCAGtt                                                            >  1:1858484/1‑50 (MQ=255)
                  cAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGACCAGtt                                                            >  1:2639680/1‑50 (MQ=255)
                  cAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGACCAGtt                                                            >  1:3007683/1‑50 (MQ=255)
                    ggCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTg                                     >  1:1672056/1‑71 (MQ=255)
                    ggCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTg                                     >  1:2545966/1‑71 (MQ=255)
                    ggCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTg                                     >  1:2179852/1‑71 (MQ=255)
                           cccaAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCt                              <  1:2685667/71‑1 (MQ=255)
                           cccaAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCt                              <  1:3216898/71‑1 (MQ=255)
                           cccaAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCt                              <  1:1256756/71‑1 (MQ=255)
                           cccaAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCt                              <  1:2375206/71‑1 (MQ=255)
                           cccaAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCt                              <  1:1601148/71‑1 (MQ=255)
                           cccaAGCAGTAGCGGCAGATAACGGCTTTCACCGCCAAGTTCACCGCAAATGCCTACCCATTTGCCCCGCt                              <  1:841567/71‑1 (MQ=255)
                           cccaAGCAGTAGCGGCAGATAACGGCTTTCACCGACCAg                                                              <  1:2596710/39‑1 (MQ=255)
                            ccaAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCGc                                                      <  1:1059601/46‑1 (MQ=255)
                            ccaAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCGc                                                      <  1:1994821/46‑1 (MQ=255)
                            ccaAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCGc                                                      <  1:1988368/46‑1 (MQ=255)
                            ccaAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCGc                                                      <  1:246944/46‑1 (MQ=255)
                            ccaAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCGc                                                      <  1:1172118/46‑1 (MQ=255)
                                        ggCAGATAACGGCTTTCACCGCCCAGTTCACCGCTAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGt                 <  1:2542177/71‑1 (MQ=255)
                                        ggCAGATAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGt                 <  1:3157772/71‑1 (MQ=255)
                                        ggCAGATAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGt                 <  1:390227/71‑1 (MQ=255)
                                         gCAGATAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGt                 <  1:2324741/70‑1 (MQ=255)
                                           aGATAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGTAAc              <  1:1143231/71‑1 (MQ=255)
                                           aGATAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGTAAc              <  1:945690/71‑1 (MQ=255)
                                           aGATAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGTAAc              <  1:3184749/71‑1 (MQ=255)
                                           aGATAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGTAAc              <  1:303894/71‑1 (MQ=255)
                                           aGATAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGTAAc              <  1:2345356/71‑1 (MQ=255)
                                           aGATAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGTAAc              <  1:2154225/71‑1 (MQ=255)
                                           aGATAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGTAAc              <  1:2492551/71‑1 (MQ=255)
                                           aGATAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGTAAc              <  1:1726059/71‑1 (MQ=255)
                                           aGATAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGTAAc              <  1:2723060/71‑1 (MQ=255)
                                            gATAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGTAAc              <  1:3135515/70‑1 (MQ=255)
                                            gATAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGTAAc              <  1:3287149/70‑1 (MQ=255)
                                             aTAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGTa                <  1:555532/67‑1 (MQ=255)
                                             aTAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGTa                <  1:904625/67‑1 (MQ=255)
                                             aTAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGTa                <  1:2031484/67‑1 (MQ=255)
                                             aTAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGTa                <  1:3164834/67‑1 (MQ=255)
                                             aTAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGTa                <  1:344034/67‑1 (MQ=255)
                                             aTAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGTa                <  1:3089519/67‑1 (MQ=255)
                                                   gCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCa                                         <  1:1293320/36‑1 (MQ=255)
                                                   gCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCa                                         <  1:1750815/36‑1 (MQ=255)
                                                   gCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCa                                         <  1:1386134/36‑1 (MQ=255)
                                                   gCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCa                                         <  1:3266467/36‑1 (MQ=255)
                                                   gCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCa                                         <  1:2233316/36‑1 (MQ=255)
                                                   gCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCa                                         <  1:99189/36‑1 (MQ=255)
                                                    cTTTCACCGCCCAGTTCACCGCAAATGCCTACCCa                                         <  1:1268398/35‑1 (MQ=255)
                                                        cACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGTAACTATTTGCTGCaa  <  1:495365/70‑1 (MQ=255)
                                                        cACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGTAACTATTTGCTGCaa  <  1:2797972/70‑1 (MQ=255)
                                                        cACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGTAACTATTTGCTGCaa  <  1:391904/70‑1 (MQ=255)
                                                        cACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGTAACTATTTGCTGCaa  <  1:747282/70‑1 (MQ=255)
                                                        cACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGTAACTATTTGCTGCaa  <  1:2406080/70‑1 (MQ=255)
                                                             |                                                                
ACTCATACTCAGCTCATCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGTAACTATTTGCTGCAA  >  W3110S.gb/2508027‑2508152

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