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 633,015 G→T 31.6% V69V (GTG→GTT)  ybdL → methionine aminotransferase, PLP‑dependent

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb633,0150GT31.6% 112.9 / 37.7 60V69V (GTG→GTT) ybdLmethionine aminotransferase, PLP‑dependent
Reads supporting (aligned to +/- strand):  ref base G (21/20);  new base T (13/6);  total (34/26)
Fisher's exact test for biased strand distribution p-value = 2.68e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-01

GCTATTTACAGGAGCGGCTGGCGCACCACGTTGCACAGGGGGCAAACCAATACGCGCCCATGACCGGCGTGCAGGCCTTGCGCGAGGCGATTGCTCAGAAAACGGAACGTTTGTATGGCTATCAACCAGATGCC  >  W3110S.gb/632945‑633078
                                                                      |                                                               
gcTATTTACAGGAGCGGCTGGCGCACCACGTTGCACAGGGGGCAAACCAATACGCGCCCATGACCGGCGTg                                                                 <  1:894956/71‑1 (MQ=255)
   aTTTACAGGAGCGGCTGGCGCACCACGTTGCACAGGGGGCAAACCAATACGCGCCCATGACCGGCGTGCAg                                                              >  1:1229910/1‑71 (MQ=255)
      tACAGGAGCGGCTGGCGCACCACGTTGCACAGGGGGCAAACCAATACGCGCCCATGACCGGCGTGCa                                                               >  1:1124322/1‑67 (MQ=255)
       aCAGGAGCGGCTGGCGCACCACGTTGCACAGGGGGCAAACCAATACGCGCCCATGACCGGCGTGCAGGCCt                                                          >  1:1020149/1‑71 (MQ=255)
        cAGGAGCGGCTGGCGCACCACGTTGCACAGGGGGCAAACCAATACGCGCCCATGACCGGCGTGCAGGCCt                                                          <  1:3072407/70‑1 (MQ=255)
           gAGCGGCTGGCGCACCACGTTGCACAGGGGGCAAACCAATACGCGCCCATGACCGGCGTTCAGGCCTTgcg                                                      >  1:2137562/1‑71 (MQ=255)
            aGCGGCTGGCGCACCACGTTGCACAGGGGGCAAACCAATACGCGCCCATGACCGGCGTTCAGGCCTTgcgc                                                     <  1:3785656/71‑1 (MQ=255)
             gCGGCTGGCGCACCACGTTGCACAGGGGGCAAACCAATACGCGCCCATGACCGGCGTGCAGGCCTTgcgc                                                     >  1:1018994/1‑70 (MQ=255)
                gCTGGCGCACCACGTTGCACAGGGGGCAAACCAATACGCGCCCATGACCGGCGTGCAGGCCTTGCGCGAg                                                  <  1:3146440/70‑1 (MQ=255)
                 cTGGCGCACCACGTTGCACAGGGGGCAAACCAATACGCGCCCATGACCGGCGTGCAGGCCTTGCGCGAGGc                                                <  1:3760607/71‑1 (MQ=255)
                 cTGGCGCACCACGTTGCACAGGGGGCAAACCAATACGCGCCCATGACCGGCGTGCAGGCCTTGCGCGAGGc                                                <  1:42486/71‑1 (MQ=255)
                           acGTTGCACAGGGGGCAAACCAATACGCGCCCATGACCGGCGTTCAGGCCTTGCGCGAGGCGa                                              >  1:2807260/1‑63 (MQ=255)
                           acGTTGCACAGGGGGCAAACCAATACGCGCCCATGACCGGCGTTCAGGCCTTGCGCGAGGCGATTGCt                                         >  1:3275943/1‑68 (MQ=255)
                            cGTTGCACAGGGGGCAAACCAATACGCGCCCATGACCGGCGTGCAGGCCTTGCGCGAGGCGATTGCTCAg                                      >  1:2138385/1‑70 (MQ=255)
                             gTTGCACAGGGGGCAAACCAATACGCGCCCATGACCGGCGTGCAg                                                              <  1:1064093/45‑1 (MQ=255)
                             gTTGCACAGGGGGCAAACCAATACGCGCCCATGACCGGCGTGCAGGCCTTGCGCGAGGCGATTGCTCAGaa                                    <  1:778891/71‑1 (MQ=255)
                             gTTGCACAGGGGGCAAACCAATACGCGCCCATGACCGGCGTGCAGGCCTTGCGCGAGGCGATTGCTCAGa                                     >  1:505950/1‑70 (MQ=255)
                              ttGCACAGGGGGCAAACCAATACGCGCCCATGACCGGCGTTCAgg                                                             <  1:2914609/45‑1 (MQ=255)
                              ttGCACAGGGGGCAAACCAATACGCGCCCATGACCGGCGTTCAGGCCTTg                                                        >  1:3605104/1‑50 (MQ=255)
                              ttGCACAGGGGGCAAACCAATACGCGCCCATGACCGGCGTTCAGGCCTTGCGCGAGGCGATTGCTCAGaa                                    >  1:4445618/1‑70 (MQ=255)
                              ttGCACAGGGGGCAAACCAATACGCGCCCATGACCGGCGTGCAGGCCTTGCGCGAGGCGATTGCTCAGaa                                    >  1:2252969/1‑70 (MQ=255)
                              ttGCACAGGGGGCAAACCAATACGCGCCCATGACCGGCGTGCAGGCCTTGCGCGAGGCGATTGCTCAGaa                                    >  1:33656/1‑70 (MQ=255)
                                gCACAGGGGGCAAACCAATACGCGCCCATGACCGGCGTGCAGGcc                                                           >  1:1023973/1‑45 (MQ=255)
                                gCACAGGGGGCAAACCAATACGCGCCCATGACCGGCGTGCAGGCCTTGCGCGAGGc                                                <  1:1839174/56‑1 (MQ=255)
                                gCACAGGGGGCAAACCAATACGCGCCCATGACCGGCGTGCAGGCCTTGCGCGAGGCGATTGCTCAGAAAAc                                 >  1:2010491/1‑71 (MQ=255)
                                 cacaGGGGGCAAACCAATACGCGCCCATGACCGGCGTTCAGGCCTTGCGCGAGGCGATTGCTCAGAAAACg                                >  1:3593696/1‑71 (MQ=255)
                                 cacaGGGGGCAAACCAATACGCGCCCATGACCGGCGTGCAGGCCt                                                          >  1:4013292/1‑45 (MQ=255)
                                      ggggCAAACCAATACGCGCCCATGACCGGCGTGCAGGCCTTGCGCGAGGCGATTGCTCAGAAAACGGCAc                            >  1:1482792/1‑70 (MQ=255)
                                      ggggCAAACCAATACGCGCCCATGACCGGCGTGCAGGCCTTGCGCGAGGCGATTGCTCAGAAAACGGAAc                            >  1:1423159/1‑70 (MQ=255)
                                       gggCAAACCAATACGCGCCCATGACCGGCGTTCAGGCCTTGCGCGAGGCGATTGCTCAGAAAACGGAACGt                          <  1:3278364/71‑1 (MQ=255)
                                         gCAAACCAATACGCGCCCATGACCGGCGTGCAGGCCTTGCGCGAGGCGa                                              >  1:2161961/1‑49 (MQ=255)
                                         gCAAACCAATACGCGCCCATGACCGGCGTGCAGGCCTTGCGCGAGGCGATTGCTCAGAAAACGGAACGttt                        >  1:979486/1‑71 (MQ=255)
                                          cAAACCAATACGCGCCCATGACCGGCGTGCAGGCCTTGCGCGAGGCGATTGCTCAGAAAACGGAACGTTTg                       <  1:1837851/71‑1 (MQ=255)
                                           aaaCCAGTACGCGCCCATGACCGGCGTTCAGGCCTTGCGCGa                                                   >  1:594037/1‑42 (MQ=38)
                                            aaCCAATACGCGCCCATGACCGGCGTGCAGGCCTTg                                                        <  1:3909883/36‑1 (MQ=255)
                                              ccAATACGCGCCCATGACCGGCGTGCAGGCCTTGCGCGAGGCGATTGCTCAGAAAACGGaa                             >  1:3673996/1‑61 (MQ=255)
                                                  tACGCGCCCATGACCGGCGTTCAGGCCTTGCGCGAGGCGATTGCTCAGaa                                    <  1:2546219/50‑1 (MQ=255)
                                                   aCGCGCCCATGACCGGCGTTCAGGCCTTGCGCGAGGCGATTGCTCAGAAAACGGAACGTTTGTATGGCTAt              >  1:2571525/1‑71 (MQ=255)
                                                   aCGCGCCCATGACCGGCGTGCAGGCCTTGCGCGAGGCGATTGCTCAGaaa                                   <  1:2405420/50‑1 (MQ=255)
                                                    cgcgCCCATGACCGGCGTTCAGGCCTTGCGCGAGGCGATTGCTCAGAAAACGGAACGTTTGTATGGCTAt              >  1:3343577/1‑70 (MQ=255)
                                                    cgcgCCCATGACCGGCGTTCAGGCCTTGCGCGAGGCGATTGCTCAGAAAACGGAACGTTTGTATGGCTAt              >  1:794621/1‑70 (MQ=255)
                                                     gcgcCCATGACCGGCGTGCAGGCCTTGCGCGAGGCGATTGCTCAGAAAACGGAACGTTTGTATGGCTATCa            <  1:1519928/71‑1 (MQ=255)
                                                       gcCCATGACCGGCGTGCAGGCCTTGCGCGAGGCGATTGCTCAGAAAACGGAACGTTTGTATGGCTATCAAc          <  1:4108826/71‑1 (MQ=255)
                                                        cccATGACCGGCGTTCAGGCCTTGCGCGAGGCGATTGCTCAGAAAACGGAACGTTTg                       <  1:1678606/57‑1 (MQ=255)
                                                        cccATGACCGGCGTTCAGGCCTTGCGCGAGGCGATTGCTCAGAAAACGGAACGTTTg                       <  1:2863953/57‑1 (MQ=255)
                                                          cATGACCGGCGTTCAGGCCTTGGGCGAGGCGATTGCTCAGAAAACGGAACGTTTGTATGGCTATCAAc          >  1:897996/1‑68 (MQ=255)
                                                           aTGACCGGCGTGCAGGCCTTGCGCGAGGCGATTGCTCAGAAAACGGAACGtt                         <  1:4271405/52‑1 (MQ=255)
                                                            tGACCGGCGTGCAGGCCTTGCGCGAGGCGATTGCTCAGAAAACgg                               <  1:1983793/45‑1 (MQ=255)
                                                              aCCGGCGTTCAGGCCTTGCGCGAGGCGATTGCTCAGaaaa                                  >  1:3620999/1‑40 (MQ=255)
                                                              aCCGGCGTTCAGGCCTTGCGCGAGGCGATTGCTCAGAAAACGGAACGTTTGTa                     >  1:3192227/1‑53 (MQ=255)
                                                              aCCGGCGTGCAGGCCTTGCGCGAGGCGATTGCTCAGAAAACGGaa                             >  1:2566715/1‑45 (MQ=255)
                                                              aCCGGCGTGCAGGCCTTGCGCGAGGCGATTGCTCAGAAAACGGAACGTTTGTATGGCTATCAACCAGa      >  1:2153483/1‑68 (MQ=255)
                                                              aCCGGCGTGCAGGCCTTGCGCGAGGCGATTGCTCAGAAAACGGAACGTTTGTATGGCTATCAACCAGATGc   >  1:2076111/1‑71 (MQ=255)
                                                              aCCGGCGTGCAGGCCTTGCGCGAGGCGATTGCTCAGAAAACGGAACGTTTGTATGGCTATCAACCAGATGc   >  1:2193421/1‑71 (MQ=255)
                                                              aCCGGCGTGCAGGCCTTGCGCGAGGCGATTGCTCAGAAAACGGAACGTTTGTATGGCTATCAACAAGATg    <  1:2335409/70‑1 (MQ=255)
                                                               ccGGCGTGCAGGCCTTGCGCGAGGCGATTGCTCAGAAAACgg                               <  1:3200384/42‑1 (MQ=255)
                                                               ccGGCGTGCAGGCCTTGCGCGAGGCGATTGCTCAGAAAACGGAACGTTTGTATGGCTATCAACCAGATGcc  <  1:1627357/71‑1 (MQ=255)
                                                                cGGCGTGCAGGCCTTGCGCGAGGCGATTGCTCAGAAAACGGAACGTTTGTa                     >  1:1966963/1‑51 (MQ=255)
                                                                cGGCGTGCAGGCCTTGCGCGAGGCGATTGCTCAGAAAACGGAACGTTTGTATGGCTATCAACCa        <  1:2142745/64‑1 (MQ=255)
                                                                cGGCGTGCAGGCCTTGCGCGAGGCGATTGCTCAGAAAACGGAACGTTTGTATGGCTATCAACCAGATGcc  <  1:4157969/70‑1 (MQ=255)
                                                                     tGCAGGCCTTGCGCGAGGCGATTGCTCAGAAAACGGa                              <  1:3966019/37‑1 (MQ=255)
                                                                      |                                                               
GCTATTTACAGGAGCGGCTGGCGCACCACGTTGCACAGGGGGCAAACCAATACGCGCCCATGACCGGCGTGCAGGCCTTGCGCGAGGCGATTGCTCAGAAAACGGAACGTTTGTATGGCTATCAACCAGATGCC  >  W3110S.gb/632945‑633078

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A