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 R1 560 56.4 4650532 94.9% 4413354 59.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 2,329,422 A→T 28.2% D215V (GAT→GTT)  atoA → acetyl‑CoA:acetoacetyl‑CoA transferase, beta subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,329,4220AT28.2% 85.0 / 38.5 53D215V (GAT→GTT) atoAacetyl‑CoA:acetoacetyl‑CoA transferase, beta subunit
Reads supporting (aligned to +/- strand):  ref base A (21/17);  new base T (6/9);  total (27/26)
Fisher's exact test for biased strand distribution p-value = 3.72e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.85e-01

GCCACCGTGCGTGCCAAAACAGAAGCTCGGTTTGAAGTCGCCGCCGATCTGAATACGCAACGGGGTGATTTATGATTGGTCGCATATCGCGTTTTATGACGCGTTTTGTCAGCCGGTGGCTTCCCGATCCACTGATCT  >  W3110S.gb/2329355‑2329492
                                                                   |                                                                      
gCCACCGTGCGTGCCAAAACAGAAGCTCGGTTTGAAGTCGCCGCCGATCTGAATACGCAACGGGGTGAtt                                                                      <  1:1268650/70‑1 (MQ=255)
  cACCGTGCGTGCCAAAACAGAAGCTCGGTTTGAAGTCGCCGCCGATCTGAATACGCAACGGGGTGATTTAt                                                                   <  1:552132/71‑1 (MQ=255)
      gtgcgtgcCAAAACAGAAGCTCGGTTTGAAGTCGCCGCCGATCTGAATACGCAACGGGGTGATTTATg                                                                  >  1:2993008/1‑68 (MQ=255)
                  aCAGAAGCTCGGTTTGAAGTCGCCGCCGATCTGAATACGCAACGGGGTGTTTTATGATTGGTCGCATATcg                                                   >  1:100639/1‑71 (MQ=255)
                   cAGAAGCTCGGTTTGAAGTCGCCGCCGATCTGAATACGCAACGGGGTGTTTTATGATTg                                                              <  1:2532780/59‑1 (MQ=255)
                   cAGAAGCTCGGTTTGAAGTCGCCGCCGATCTGAATACGCAACGGGGTGTTTTATGATTg                                                              <  1:205956/59‑1 (MQ=255)
                    aGAAGCTCGGTTTGAAGTCGCCGCCGATCTGAATACGCAACGGGGTGATTTATGATTGGTCGCATATcgcg                                                 >  1:3385672/1‑71 (MQ=255)
                    aGAAGCTCGGTTTGAAGTCGCCGCCGATCTGAATACGCAACGGGGTGATTTATGATTGGTCGCATATcgcg                                                 >  1:2584782/1‑71 (MQ=255)
                       aGCTCGGTTTGAAGTCGCCGCCGATCTGAATACGCAACGGGGTGTTTTATGATTGGTCGCATATCGCGttt                                              <  1:735964/71‑1 (MQ=255)
                          tCGGTTTGAAGTCGCCGCCGATCTGAATACGCAACGGGGTGAttt                                                                     <  1:1594231/45‑1 (MQ=255)
                               ttGAAGTCGCCGCCGATCTGAATACGCAACGGGGTGATTTATGATTGGTCGCATATCGCGTTTTATGAc                                        >  1:1165444/1‑69 (MQ=255)
                                tGAAGTCGCCGCCGATCTGAATACGCAACGGGGTGATTTAt                                                                   <  1:1947709/41‑1 (MQ=255)
                                  aaGTCGCCGCCGATCTGAATACGCAACGGGGTGTTTTATGATTGGTCGCATATCGCGTTTTATGACGCGtt                                   >  1:2905973/1‑71 (MQ=255)
                                  aaGTCGCCGCCGATCTGAATACGCAACGGGGTGATTTATGATTGGTCGCATATCGCGTTTTa                                            >  1:3238898/1‑62 (MQ=255)
                                    gTCGCCGCCGATCTGAATACGCAACGGGGTGTTTTATGATTGGTCGCATATCGCGTTTTATGACGCGtttt                                 <  1:251152/71‑1 (MQ=255)
                                     tCGCCGCCGATCTGAATACGCAACGGGGTGATTTAt                                                                   <  1:4428832/36‑1 (MQ=255)
                                     tCGCCGCCGATCTGAATACGCAACGGGGTGATTTATGATTg                                                              <  1:2494568/41‑1 (MQ=255)
                                     tCGCCGCCGATCTGAATACGCAACGGGGTGATTTATGATTGGTCGCATATCGCGTTTTATGACGCGTTTTg                                <  1:1634738/71‑1 (MQ=255)
                                     tCGCCGCCGATCTGAATACGCAACGGGGTGATTTATGATTGGTCGCATATCGCGTTTTATGACGCGTTTTg                                <  1:279056/71‑1 (MQ=255)
                                       gccgccGATCTGAATACGCAACGGGGTGTTTTATGATTGGTCGCATATCGCGTTTTATGACGCGTTTTGTc                              <  1:1186486/71‑1 (MQ=255)
                                       gccgccGATCTGAATACGCAACGGGGTGATTTATGa                                                                 >  1:1172067/1‑36 (MQ=255)
                                       gccgccGATCTGAATACGCAACGGGGTGATTTATGATTGGTCGCata                                                      >  1:769511/1‑47 (MQ=255)
                                       gccgccGATCTGAATACGCAACGGGGTGATTTATGATTGGTCGCATATCGCGTTTTATGACGCGTTTTGt                               >  1:2578438/1‑70 (MQ=255)
                                       gccgccGATCTGAATACGCAACGGGGTGATTTATGATTGGTCGCATATCGCGTTTTATGACGCGTTTTGt                               >  1:1870181/1‑70 (MQ=255)
                                       gccgccGATCTGAATACGCAACGGGGTGATTTATGATTGGTCGCATATCGCGTTTTATGACGCGTTTTGt                               >  1:516741/1‑70 (MQ=255)
                                       gccgccGATCTGAATACGCAACGGGGTGATTTATGATTGGTCGCATATCGCGTTTTATGACGCGTTTTGt                               >  1:3229594/1‑70 (MQ=255)
                                              aTCTGAATACGCAACGGGGTGTTTTATGATTGGTCGCATATCGCGTTTTATGACGCGTTTTGt                               <  1:3379018/63‑1 (MQ=255)
                                               tCTGAATACGCAACGGGGTGTTTTATGATTGGTCGCATATCGCGttt                                              <  1:135559/47‑1 (MQ=255)
                                               tCTGAATACGCAACGGGGTGATTTATGATTGGTCGCATATCGCGTTTTATGACGCGttt                                  >  1:485167/1‑59 (MQ=255)
                                                cTGAATACGCAACGGGGTGTTTTATGATTGGTCGCATATCGCGTTTTATGACGCGTTTTGt                               <  1:283331/61‑1 (MQ=255)
                                                cTGAATACGCAACGGGGTGATTTATGATTGGTCGCATATCGCGTTTTATGACGCGtttt                                 >  1:342006/1‑59 (MQ=255)
                                                cTGAATACGCAACGGGGTGATTTATGATTGGTCGCATATCGCGTTTTATGACGCGttt                                  >  1:2452358/1‑58 (MQ=255)
                                                cTGAATACGCAACGGGGTGATTTATGATTGGTCGCATATCGCGTTTTATGACGCGTTTTGTCAGCCgg                        >  1:2665056/1‑68 (MQ=255)
                                                 tGAATACGCAACGGGGTGATTTATGATTGGTCGCATATCGCGTTTTa                                            <  1:1293845/47‑1 (MQ=255)
                                                 tGAATACGCAACGGGGTGATTTATGATTGGTCGCATATCGCGTTTTATGACGCGtttt                                 <  1:1791963/58‑1 (MQ=255)
                                                   aaTACGCAACGGGGTGATTTATGATTGGTCGCATATCGCGTTTTATg                                          >  1:1415912/1‑47 (MQ=255)
                                                   aaTACGCAACGGGGTGATTTATGATTGGTCGCATATCGCGTTTTATGACGCGtt                                   >  1:2413849/1‑54 (MQ=255)
                                                   aaTACGCAACGGGGTGATTTATGATTGGTCGCATATCGCGTTTTATGACGCGTTTTGTCAGCCGGTGGCtt                  >  1:851314/1‑71 (MQ=255)
                                                   aaTACGCAACGGGGTGATTTATGATTGGTCGCATATCGCGTTTTATGACGCGTTTTGTCAGCCGGTGGCtt                  >  1:845834/1‑71 (MQ=255)
                                                   aaTACGCAACGGGGTGATTTATGATTGGTCGCATATCGCGTTTTATGACGCGTTTTGTCAGCCGGTGGCtt                  <  1:1566094/71‑1 (MQ=255)
                                                    aTACGCAACGGGGTGATTTATGATTGGTCGCATATCGCGTTTTATGACGCGTTTTGTCAGCCGGTGGCTTc                 >  1:804530/1‑71 (MQ=255)
                                                    aTACGCAACGGGGTGATTTATGATTGGTCGCATATCGCGTTTTATGACGCGTTTTGTCAGCCGGTGGCTTc                 >  1:3121256/1‑71 (MQ=255)
                                                          aaCGGGGTGTTTTATGATTGGTCGCATATCGCGTTTTATGACGCGtttt                                 <  1:1288776/49‑1 (MQ=255)
                                                          aaCGGGGTGTTTTATGATTGGTCGCATATCGCGTTTTATGACGCGTTTTGTCAGCCGGTGGCTTCCCGATc           >  1:625668/1‑71 (MQ=255)
                                                          aaCGGGGTGATTTATGATTGGTCGCATATCGCGTTTTATGACGCGTTTTGTCAGCCGGTGGCTTCCCGATc           <  1:2793863/71‑1 (MQ=255)
                                                          aaCGGGGTGATTTATGATTGGTCGCATATCGCGTTTTATGACGCGTTTTGTCAGCCGGTGGCTTCCCGATc           <  1:730325/71‑1 (MQ=255)
                                                             ggggTGTTTTATGATTGGTCGCATATCGCGTTTTATg                                          >  1:4637119/1‑37 (MQ=255)
                                                             ggggTGTTTTATGATTGGTCGCATATCGCGTTTTATGa                                         >  1:560585/1‑38 (MQ=255)
                                                             ggggTGTTTTATGATTGGTCGCATATCGCGTTTTATGa                                         >  1:2873546/1‑38 (MQ=255)
                                                              gggTGATTTATGATTGGTGGCATATCGCGTTTTATGACGCGTTTTGTCAGcc                          <  1:3337369/52‑1 (MQ=255)
                                                               ggTGATTTATGATTGGTCGCATATCGCGTTTTATGACGCGTTTTGTCAGCCGGTGGCTTCCCGATCCACTg      <  1:4595280/71‑1 (MQ=255)
                                                                 tGATTTATGATTGGTCGCATATCGCGTTTTATGACGCGTTTTGTCAGCCGGTg                      <  1:62500/53‑1 (MQ=255)
                                                                 tGATTTATGATTGGTCGCATATCGCGTTTTATGACGCGTTTTGTCAGCCGGTGGCTTCCCGATCCACTg      <  1:37990/69‑1 (MQ=255)
                                                                   aTTTATGATTGGTCGCATATCGCGTTTTATGACGCGttt                                  >  1:3467010/1‑39 (MQ=255)
                                                                   aTTTATGATTGGTCGCATATCGCGTTTTATGACGCGTTTTGTCAGCCGGTGGc                    >  1:3621458/1‑53 (MQ=255)
                                                                   aTTTATGATTGGTCGCATATCGCGTTTTATGACGCGTTTTGTCAGCCGGTGGCTTCCCGATCCTCTGATCt  >  1:3692154/1‑71 (MQ=255)
                                                                   aTTTATGATTGGTCGCATATCGCGTTTTATGACGCGTTTTGTCAGCCGGTGGCTTCCCGATCCACTGAt    >  1:3679512/1‑69 (MQ=255)
                                                                   |                                                                      
GCCACCGTGCGTGCCAAAACAGAAGCTCGGTTTGAAGTCGCCGCCGATCTGAATACGCAACGGGGTGATTTATGATTGGTCGCATATCGCGTTTTATGACGCGTTTTGTCAGCCGGTGGCTTCCCGATCCACTGATCT  >  W3110S.gb/2329355‑2329492

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