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
A5 F21 I0 R2 316 65.6 5147759 97.4% 5013917 60.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 2,972,729 T→C 46.1% S648G (AGC→GGC)  aas ← fused 2‑acylglycerophospho‑ethanolamine acyl transferase and acyl‑acyl carrier protein synthetase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,972,7290TC46.1% 7.0 / 109.5 76S648G (AGC→GGC) aasfused 2‑acylglycerophospho‑ethanolamine acyl transferase and acyl‑acyl carrier protein synthetase
Reads supporting (aligned to +/- strand):  ref base T (22/19);  new base C (19/16);  total (41/35)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.92e-01

TGCAACTTATCGCGCGTCAGTTCGTTATCTGTGGTGAAAAGCACCAGTGCCTCGCCTTTGCTGGCATCGCTCTTAATCGCAGTGGCATGGACTTTATCTGGCGAAACACCAAGTGCCAGTTGTTCCACCATTTCCAGC  >  W3110S.gb/2972659‑2972796
                                                                      |                                                                   
tGCAACTTATCGCGCGTCAGTTCGTTATCTGTGGTGAAAAGCACCAGTGCCTCGCCTTTGCTGGCATCGct                                                                     >  1:3148887/1‑71 (MQ=255)
   aaCTTATCGCGCGTCAGTTCGTTATCTGTGGTGAAAAGCACCAGTGCCTCGCCTTTGCTGGCATCGCTCtt                                                                  <  1:4786714/71‑1 (MQ=255)
     cTTATCGCGCGTCAGTTCGTTATCTGTGGTGAAAAGCACCAGTGCCTCGCCTTTGCTGGCATCGCCCTTaa                                                                >  1:2960524/1‑71 (MQ=255)
     cTTATCGCGCGTCAGTTCGTTATCTGTGGTGAAAAGCACCAGTGCCTCGCCTTTGCTGGCATCGCCCTTaa                                                                >  1:2737215/1‑71 (MQ=255)
      ttATCGCGCGTCAGTTCGTTATCTGTGGTGAAAAGCACCAGTGCCTCGCCTTTGCTGGCATCGCTCTTAAt                                                               >  1:336917/1‑71 (MQ=255)
       tATCGCGCGTCAGTTCGTTATCTGTGGTGAAAAGCACCAGTGCCTCGCCTTTGCTGGCATCGCCCTTa                                                                 >  1:2770477/1‑68 (MQ=255)
       tATCGAGCGTCAGTTCGTTATCTGTGGTGAAAAGCAACAGTGCCTCGCCTTTGCTGGCATCGCCCTTa                                                                 >  1:3928891/1‑68 (MQ=255)
         tCGCGCGTCAGTTCGTTATCTGTGGTGAAAAGCACCAGTGCCTCGCCTTTGCTGGCATCGCTCTTAATCg                                                             <  1:1912984/70‑1 (MQ=255)
         tCGCGCGTCAGTTCGTTATCTGTGGTGAAAAGCACCAGTGCCTCGCCTTTGCTGGCATCGCCCTTAATCGc                                                            <  1:817277/71‑1 (MQ=255)
         tCGCGCGTCAGTTCGTTATCTGTGGTGAAAAGCACCAGTGCCTCGCCTTTGCTGGCATCGCCCTTAATCGc                                                            <  1:612403/71‑1 (MQ=255)
               gTCAGTTCGTTATCTGTGGTGAAAAGCACCAGTGCCTCGCCTTTGCTGGCATCGCTCTTAATCGCAGTgg                                                       >  1:1867200/1‑70 (MQ=255)
                tCAGTTCGTTATCTGTGGTGAAAAGCACCAGTGCCTCGCCTTTGCTGGCATCGCTCTTAATCGCAGTGGCa                                                     <  1:4324412/71‑1 (MQ=255)
                 cAGTTCGTTATCTGTGGTGAAAAGCACCAGTGCCTCGCCTTTGCTGGCATCGCTCTTAATCGCAGTGGCAt                                                    >  1:4326355/1‑71 (MQ=255)
                  aGTTCGTTATCTGTGGTGAAAAGCACCAGTGCCTCGCCTTTGCTGGCATCGCTCTTAATCGCAGTGGCAt                                                    <  1:4851887/70‑1 (MQ=255)
                  aGTTCGTTATCTGTGGTGAAAAGCACCAGTGCCTCGCCTTTGCTGGCATCGCCCTTAATCGCAGTGGCATg                                                   <  1:4427554/71‑1 (MQ=255)
                    ttCGTTATCTGTGGTGAAAAGCACCAGTGCCTCGCCTTTGCTGGCATCGCTCTTAATCGCAg                                                          >  1:5008700/1‑62 (MQ=255)
                    ttCGTTATCTGTGGTGAAAAGCACCAGTGCCTCGCCTTTGCTGGCATCGCTCTTAATCGCAGt                                                         >  1:3669228/1‑63 (MQ=255)
                       gTTATCTGTGGTGAAAAGCACCAGTGCCTCGCCTTTGCTGGCATCGCTCTTAATCGCAGTGGCATGGACtt                                              >  1:1704818/1‑71 (MQ=255)
                          aTCTGTGGTGAAAAGCACCAGTGCCTCGCCTTTGCTGGCATCGCTCTTAATCGCAGTGGCATGGACTTTa                                            <  1:4856998/70‑1 (MQ=255)
                          aTCTGTGGTGAAAAGCACCAGTGCCTCGCCTTTGCTGGCATCGCTCTTAATCGCAGTGGCATGGACTTTAt                                           >  1:4611148/1‑71 (MQ=255)
                          aTCTGTGGTGAAAAGCACCAGTGCCTCGCCTTTGCTGGCATCGCCCTTAATCGCAGTg                                                        >  1:4171018/1‑58 (MQ=255)
                          aTCTGTGGTGAAAAGCACCAGTGCCTCGCCTTTGCTGGCATCGCCCTTAATCGCAGTg                                                        >  1:1986192/1‑58 (MQ=255)
                           tCTGTGGTGAAAAGCACCAGTGCCTCGCCTTTGCTGGCATCGCCCTTAATCGCAGTGGCATGGACTTTATc                                          >  1:4545521/1‑71 (MQ=255)
                           tCTGTGGTGAAAAGCACCAGTGCCTCGCCTTTGCTGGCATCGCCCTTAATCGCAGTGGCATGGACTTTATc                                          >  1:798152/1‑71 (MQ=255)
                           tCTGTGGTGAAAAGCACCAGTGCCTCGCCTTTGCTGGCATCGCCCTTAATCGCAGTGGCATGGACTTTATc                                          >  1:5144837/1‑71 (MQ=255)
                               tggtgAAAAGCACCAGTGCCTCGCCTTTGCTGGCATCGCTCTTaa                                                                >  1:2686062/1‑45 (MQ=255)
                               tggtgAAAAGCACCAGTGCCTCGCCTTTGCTGGCATCGCTCTTAATCGCAGTGGCATGGACTTTATCt                                         <  1:4230949/68‑1 (MQ=255)
                               tggtgAAAAGCACCAGTGCCTCGCCTTTGCTGGCATCGCTCTTAATCGCAGTGGCATGGACTTTATCTg                                        <  1:4047131/69‑1 (MQ=255)
                                 gtgAAAAGCACCAGTGCCTCGCCTTTGCTGGCATCGCTCTTAATCGCAGTTGc                                                      <  1:4066304/53‑1 (MQ=255)
                                 gtgAAAAGCACCAGTGCCTCGCCTTTGCTGGCATCGCCCTTAATCGCAGTGGCATg                                                   <  1:4762458/56‑1 (MQ=255)
                                 gtgAAAAGCACCAGTGCCTCGCCTTTGCTGGCATCGCCCTTAATCGCAGTGGCATg                                                   <  1:2631005/56‑1 (MQ=255)
                                 gtgAAAAGCACCAGTGCCTCGCCTTTGCTGGCATCGCCCTTAATCGCAGTGGCATg                                                   <  1:2515060/56‑1 (MQ=255)
                                 gtgAAAAGCACCAGTGCCTCGCCTTTGCTGGCATCGCCCTTAATCGCAGTGGCATg                                                   <  1:1131309/56‑1 (MQ=255)
                                 gtgAAAAGCACCAGTGCCTCGCCTTTGCTGGCATCGCCCTTAATCGCAGTGGCATGGACTTTATCTGGCGa                                    <  1:2113574/71‑1 (MQ=255)
                                 gtgAAAAGCACCAGTGCCTCGCCTTTGCTGGCATCGCCCTTAATCGCAGTGGCATGGACTTTATCTCGCGa                                    <  1:2130138/71‑1 (MQ=255)
                                  tgAAAAGCACCAGTGCCTCGCCTTTGCTGGCATCGCTCTTAATCGCAGTGGCATGGACt                                               <  1:2506202/59‑1 (MQ=255)
                                  tgAAAAGCACCAGTGCCTCGCCTTTGCTGGCATCGCCCTTAATCGCAGTGGCATg                                                   <  1:2915599/55‑1 (MQ=255)
                                    aaaaGCACCAGTGCCTCGCCTTTGCTGGCATCGCTCTTAATCGCAGTGGCATGGACTTTATCTGGCGaaa                                  >  1:4339652/1‑70 (MQ=255)
                                    aaaaGCACCAGTGCCTCGCCTTTGCTGGCATCGCCCtt                                                                  <  1:3551999/38‑1 (MQ=255)
                                    aaaaGCACCAGTGCCTCGCCTTTGCTGGCATCGCCCtt                                                                  <  1:1867447/38‑1 (MQ=255)
                                    aaaaGCACCAGTGCCTCGCCTTTGCTGGCATCGCCCTTAATCGc                                                            <  1:2792917/44‑1 (MQ=255)
                                    aaaaGCACCAGTGCCTCGCCTTTGCTGGCATCGCCCTTAATCGCAGTGGCATGGACTTTATCTGGc                                      <  1:622368/66‑1 (MQ=255)
                                     aaaGCACCAGTGCCTCGCCTTTGCTGGCATCGCTCTTAATCGCAg                                                          >  1:4041752/1‑45 (MQ=255)
                                     aaaGCACCAGTGCCTCGCCTTTGCTGGCATCGCTCTTAATCGCAg                                                          >  1:4838563/1‑45 (MQ=255)
                                       aGCACCAGTGCCTCGCCTTTGCTGGCATCGCTCTTAATCGCa                                                           >  1:1298024/1‑42 (MQ=255)
                                       aGCACCAGTGCCTCGCCTTTGCTGGCATCGCTCTTAATCGCa                                                           >  1:4848742/1‑42 (MQ=255)
                                       aGCACCAGTGCCTCGCCTTTGCTGGCATCGCTCTTAATCGCAGTGGCATGGACTTTATCTGGCGAAACAcc                              <  1:4582178/71‑1 (MQ=255)
                                       aGCACCAGTGCCTCGCCTTTGCTGGCATCGCCCTTAATCGCAGTGGCATGGACTTTATCTGGCGAAacac                               >  1:5120379/1‑70 (MQ=255)
                                          aCCAGTGCCTCGCCTTTGCTGGCATCGCTCTTAATCGCAGTgg                                                       >  1:701934/1‑43 (MQ=255)
                                          aCCAGTGCCTCGCCTTTGCTGGCATCGCTCTTAATCGCAGTGGCATGGACTTTATCTGGCGAAACACCAAg                           >  1:2780286/1‑71 (MQ=255)
                                          aCCAGTGCCTCGCCTTTGCTGGCATCGCTCTTAATCGCAGTGGCATGGACTTTATCTGGCGAAACACCAAg                           >  1:2712469/1‑71 (MQ=255)
                                           ccAGTGCCTCGCCTTTGCTGGCATCGCTCTTAATCGCAGTGGCATGGACTTTATCTGGCGa                                    <  1:5121947/61‑1 (MQ=255)
                                             aGTGCCTCGCCTTTGCTGGCATCGCCCTTAATCGCAGTGGCATGGACTTTATCTGGCGaaa                                  >  1:3472321/1‑61 (MQ=255)
                                             aGTGCCTCGCCTTTGCTGGCATCGCCCTTAATCGCAGTGGCATGGACTTTATCTGGCGaaa                                  >  1:884370/1‑61 (MQ=255)
                                             aGTGCCTCGCCTTTGCTGGCATCGCCCTTAATCGCAGTGGCATGGACTTTATCTGGCGaaa                                  >  1:454483/1‑61 (MQ=255)
                                              gTGCCTCGCCTTTGCTGGCATCGCTCTTAATCGCAGTGGCATGGACTTTATCTGGCGaaa                                  >  1:1849740/1‑60 (MQ=255)
                                                gCCTCGCCTTTGCTGGCATCGCCCTTAATCGCGGTGGCATGGACTTTATCTGGCGAAACACCAAGTGCCAg                     >  1:1127310/1‑71 (MQ=255)
                                                gCCTCGCCTTTGCTGGCATCGCCCTTAATCGCAGTGGCATGGACTTTATCTGGCGAAACACCAAGTGCCAg                     >  1:5097339/1‑71 (MQ=255)
                                                 ccTCGCCTTTGCTGGCATCGCTCTTAATCGCAGTGGCATGGACTTTATCTGGCGAAACACCAAGTGCCAgt                    <  1:1687135/71‑1 (MQ=255)
                                                  cTCGCCTTTGCTGGCATCGCTCTTAATCGCAGTGGCATGGACTTTATCTGGCGAAACACCAAGTGCCAgt                    <  1:1478209/70‑1 (MQ=255)
                                                     gCCTTTGCTGGCATCGCCCTTAATCGCAGTGGCATGGACTTTATCTGGCGAAACACCAAGTGCCAgttgtt                >  1:4965639/1‑71 (MQ=255)
                                                          tGCTGGCATCGCCCTTAATCGCAGTGGCATGGACTTTATCTGGCGAAACACCAAGTGCCAGTTGTTccac            >  1:2266396/1‑70 (MQ=255)
                                                          tGCTGGCATCGCCCTTAATCGCAGTGGCATGGACTTTATCTGGCGAAACACCAAGTGCCAGTTGTTcca             >  1:2012209/1‑69 (MQ=255)
                                                          tGCTGGCATCGCCCTTAATCGCAGTGGCATGGACTTTATCTGGCGAAACACCAAGTGCCAGTTGTTcca             <  1:5072635/69‑1 (MQ=255)
                                                               gCATCGCTCTTAATCGCAGTGGCATGGACTTTATCTGGCGAAACACCAAGTGCCAGTTGTTCCACCATTTc      <  1:2802579/71‑1 (MQ=255)
                                                               gCATCGCCCTTAATCGCAGTGGCATGGACTTTATCTGGCGAAACACCAAGTGCCAGTTGTTccac            >  1:2596231/1‑65 (MQ=255)
                                                               gCATCGCCCTTAATCGCAGTGGCATGGACTTTATCTGGCGAAACACCAAGTGCCAGTTGTTCCACCATTTc      <  1:5010810/71‑1 (MQ=255)
                                                                cATCGCTCTTAATCGCAGTGGCATGGACTTTATCTGGCGAAACACCAAGTGCCAGTTGTTCCACCATTTcc     <  1:3791755/71‑1 (MQ=255)
                                                                  tCGCTCTTAATCGCAGTGGCATGGACTTTATCTGGCGAAACACCa                             <  1:5007271/45‑1 (MQ=255)
                                                                  tCGCTCTTAATCGCAGTGGCATGGACTTTATCTGGCGAAACACCa                             <  1:1949736/45‑1 (MQ=255)
                                                                    gCTCTTAATCGCAGTGGCATGGACTTTATCTGGCg                                     >  1:1491058/1‑35 (MQ=255)
                                                                    gCTCTTAATCGCAGTGGCATGGACTTTATCTGGCGa                                    <  1:906999/36‑1 (MQ=255)
                                                                    gCTCTTAATCGCAGTGGCATGGACTTTATCTGGCGa                                    <  1:3302524/36‑1 (MQ=255)
                                                                    gCTCTTAATCGCAGTGGCATGGACTTTATCTGGCGAAACACCAAGTGCCAgt                    >  1:202097/1‑52 (MQ=255)
                                                                    gCTCTTAATCGCAGTGGCATGGACTTTATCTGGCGAAACACCAAGTGCCAGTTGTTCCACCATTTCCAGc  >  1:3175910/1‑70 (MQ=255)
                                                                    gCTCTTAATCGCAGTGGCATGGACTTTATCTGGCGAAACACCAAGTGCCAGTTGTTCCACCATTTCCAGc  >  1:259131/1‑70 (MQ=255)
                                                                    gCTCTTAATCGCAGTGGCATGGACTTTATCTGGCGAAACACCAAGTGCCAGTTGTTCCACCATTTCCAGc  >  1:2457227/1‑70 (MQ=255)
                                                                     ctctTAATCGCAGTGGCATGGACTTTATCTGGCGa                                    <  1:2083019/35‑1 (MQ=255)
                                                                      |                                                                   
TGCAACTTATCGCGCGTCAGTTCGTTATCTGTGGTGAAAAGCACCAGTGCCTCGCCTTTGCTGGCATCGCTCTTAATCGCAGTGGCATGGACTTTATCTGGCGAAACACCAAGTGCCAGTTGTTCCACCATTTCCAGC  >  W3110S.gb/2972659‑2972796

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