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 F8 I0 R2 296 77.6 4260404 88.1% 3753415 61.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 879,563 T→C 47.2% Y18H (TAT→CAT)  yciM → conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE879,5630TC47.2% 2.5 / 75.8 53Y18H (TAT→CAT) yciMconserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (14/14);  new base C (17/8);  total (31/22)
Fisher's exact test for biased strand distribution p-value = 2.65e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GAAGGAATAACTTTCTATGCTGGAGTTGTTGTTTCTGCTTTTGCCTGTAGCCGCTGCCTATGGCTGGTATATGGGCCGCAGAAGTGCGCAACAAAACAAGCAAGATGAAGCCAACCGCTTGTCGCGTGATTAC  >  minE/879496‑879628
                                                                   |                                                                 
gAAGGAATAACTTTCTATGCTGGAGTTGTTGTTTCTGCTTTTGCCTGTAGCCGCTGCCTATGGCTGGtata                                                                <  1:1157970/71‑1 (MQ=255)
gAAGGAATAACTTTCTATGCTGGAGTTGTTGTTTCTGCTTTTGCCTGTAGCCGCTGCCTATGGCTGGtata                                                                <  1:2653772/71‑1 (MQ=255)
 aaGGAATAACTTTCTATGCTGGAGTTGTTGTTTCTGCTTTTGCCTGTAGCCGCTGCCTATGGCTGGCatat                                                               >  1:115787/1‑71 (MQ=255)
 aaGGAATAACTTTCTATGCTGGAGTTGTTGTTTCTGCTTTTGCCTGTAGCCGCTGCCTAAGGCTGGCatat                                                               >  1:2147602/1‑71 (MQ=255)
    gAATAACTTTCTATGCTGGAGTTGTTGTTTCTGCTTTTGCCTGTAGCCGCTGCCTATGGCTGGTATATggg                                                            >  1:910574/1‑71 (MQ=255)
    gAATAACTTTCTATGCTGGAGTTGTTGTTTCTGCTTTTGCCTGTAGCCGCTGCCTATGGCTGGTATATggg                                                            >  1:91090/1‑71 (MQ=255)
    gAATAACTTTCTATGCTGGAGTTGTTGTTTCTGCTTTTGCCTGTAGCCGCTGCCTATGGCTGGTATATggg                                                            >  1:2292438/1‑71 (MQ=255)
    gAATAACTTTCTATGCTGGAGTTGTTGTTTCTGCTTTTGCCTGTAGCCGCTGCCTATGGCTGGTATATgg                                                             >  1:1795986/1‑70 (MQ=255)
     aaTAACTTTCTATGCTGGAGTTGTTGTTTCTGCTTTTGCCTGTAGCCGCTGCCTATGGCTGGCATATggg                                                            >  1:804539/1‑70 (MQ=255)
     aaTAACTTTCTATGCTGGAGTTGTTGTTTCTGCTTTTGCCTGTAGCCGCTGCCTATGGCTGGCATATGGGc                                                           >  1:1262560/1‑71 (MQ=255)
         aCTTTCTATGCTGGAGTTGTTGTTTCTGCTTTTGCCTGTAGCCGCTGCCTATGGCTGGCATATGGGCCg                                                         >  1:105634/1‑69 (MQ=255)
            ttCTATGCTGGAGTTGTTGTTTCTGCTTTTGCCTGTAGCCGCTGCCTATGGCTGGTATATGGGCCGCAg                                                      >  1:462989/1‑69 (MQ=255)
            ttCTATGCTGGAGTTGTTGTTTCTGCTTTTGCCTGTAGCCGCTGCCTATGGCTGGTATATGGGCCGCAg                                                      >  1:3014267/1‑69 (MQ=255)
                        gttgttgttTCTGCTTTTGCCTGTAGCCGCTGCCTATGGCTGGCATATGGGCCGCAGAAGTGCGcaacaa                                         >  1:855402/1‑70 (MQ=255)
                        gttgttgttTCTGCTTTTGCCTGTAGCCGCTGCCTATGGCTGGCATATGGGCCGCAGAAGTGCGcaacaa                                         >  1:3294551/1‑70 (MQ=255)
                           gttgttTCTGCTTTTGCCTGTAGCCGCTGCCTATGGCTGGTATATGGGCCGCAGAAGTGCGCaacaaaac                                      >  1:4113971/1‑70 (MQ=255)
                           gttgttTCTGCTTTTGCCTGTAGCCGCTGCCTATGGCTGGCATATGGGCCGCa                                                       >  1:2212503/1‑53 (MQ=255)
                               tttCTGCTTTTGCCTGTAGCCGCTGCCTATGGCTGGCATATGGGCCGCAGAAGTGCGCAACAAAAcaagc                                  <  1:1937785/70‑1 (MQ=255)
                               tttCTGCTTTTGCCTGTAGCCGCTGCCTATGGCTGGCATATGGGCCGCAGAAGTGCGCAACAAAAcaagc                                  <  1:4049072/70‑1 (MQ=255)
                               tttCTGCTTTTGCCTGTAGCCGCTGCCTATGGCTGGCATATGGGCCGCAGAAGTGCGCAACAAAAcaagc                                  <  1:4053722/70‑1 (MQ=255)
                                 tCTGCTTTTGCCTGTAGCCGCTGCCTATGGCTGGTATATGGGCCGCAGAAGTGCGCAACAAAAcaagcaa                                <  1:1618267/70‑1 (MQ=255)
                                 tCTGCTTTTGCCTGTAGCCGCTGCCTATGGCTGGTATATGGGCCGCAGAAGTGCGCAACAAAAcaagc                                  >  1:2210886/1‑68 (MQ=255)
                                  cTGCTTTTGCCTGTAGCCGCTGCCTATGGCTGGTATATGGGCCGCAGAAGTGCGCAACAAAAcaagcaag                               <  1:2661596/70‑1 (MQ=255)
                                  cTGCTTTTGCCTGTAGCCGCTGCCTATGGCTGGTATATGGGCCGCAGAAGTGCGCAACAAAAcaagc                                  >  1:2442728/1‑67 (MQ=255)
                                   tGCTTTTGCCTGTAGCCGCTGCCTATGGCTGGTATATGGGCCGCAGAAGTGCGCAACAAAACAAGCAAGAt                             >  1:974397/1‑71 (MQ=255)
                                   agCTTTTGCCTCTAGCCGCTGCCTATGGCAGGTAAATGGGCCGCAGaa                                                    >  1:1285699/2‑48 (MQ=255)
                                     cTTTTGCCTGTAGCCGCTGCCTATGGCTGGTATATGGGCCGCAGAAGTGCGCAACAAAACAAGCAAGATg                            <  1:3290590/70‑1 (MQ=255)
                                     cTTTTGCCTGTAGCCGCTGCCTATGGCTGGCATATGGGCCGCAGAAGTGCGCAACAAAACAAGCAAGAt                             <  1:2251847/69‑1 (MQ=255)
                                         tGCCTGTAGCCGCTGCCTATGGCTGGCATATGGGCCGCAGAAGTGCGCAACAAAACAAGCAAGATGAAGc                        >  1:1623511/1‑70 (MQ=255)
                                         tGCCTGTAGCCGCTGCCTATGGCTGGCATATGGGCCGCAGAAGTGCGCAACAAAACAAGCAAGATGAAGc                        >  1:4051665/1‑70 (MQ=255)
                                         tGCCTGTAGCCGCTGCCTATGGCTGGCATATGGGCCGCAGAAGTGCGCAACAAAACAAGCAAGATGAAGc                        >  1:1826435/1‑70 (MQ=255)
                                           ccTGTAGTCGCTGCCTATGGCTGGTATATGGGCCGCAGAAGTGCGCAACAAAACAAGCAAGATGAAGCCa                      <  1:167047/70‑1 (MQ=255)
                                           ccTGTAGCCGCTGCCTATGGCTGGCATATGGGCCGCAGAAGTGCGCAACAAAACAAGCAAGATGAAGCCa                      <  1:2975182/70‑1 (MQ=255)
                                           ccTGTAGCCGCTGCCTATGGCTGGCATATGGGCCGCAGAAGTGCGCAACAAAACAAGCAAGATGAAGCCa                      <  1:3229678/70‑1 (MQ=255)
                                            cTGTAGCCGCTGCCTATGGCTGGTATATGGGCCGCAGAAGTGCGCAACAAAAcaagcaa                                <  1:1886098/59‑1 (MQ=255)
                                            cTGTAGCCGCTGCCTATGGCTGGTATATGGGCCGCAGAAGTGCGCAACAAAAcaagcaa                                <  1:1872479/59‑1 (MQ=255)
                                            cTGTAGCCGCTGCCTATGGCTGGTATATGGGCCGCAGAAGTGCGCAACAAAAcaagcaa                                <  1:3685451/59‑1 (MQ=255)
                                            cTGTAGCCGCTGCCTATGGCTGGTATATGGGCCGCAGAAGTGCGCAACAAAAcaagcaa                                <  1:377884/59‑1 (MQ=255)
                                               tAGCCGCTGCCTATGGCTGGTATATGGGCCGCAGAAGTGCGCAACAAAACAAGCAAGATGAAGCCAAcc                   <  1:555219/69‑1 (MQ=255)
                                               tAGCCGCTGCCTATGGCTGGCATATGGGCCGCAGAAGTGCGCAACAAAACAAGCAAGATGAAGCCAAcc                   <  1:3057552/69‑1 (MQ=255)
                                                 gCCGCTGCCTATGGCTGGTATATGGGCCGCAGAAGTGCGCAACAAAACAAGCAAGATGAAGCCAACCGCtt               <  1:3947157/71‑1 (MQ=255)
                                                 gCCGCTGCCTATGGCTGGTATATGGGACGCAGAAGTGCGCAACAAAACAAGCAAGATGAAGCCAACCGCtt               <  1:1601959/71‑1 (MQ=255)
                                                 gCCGCTGCCTATGGCTGGCATATGGGCCGCAGAAGTGCGCAACAAAACAAGCAAGATGAAGCCAACCGCtt               >  1:3934476/1‑71 (MQ=255)
                                                 gCCGCTGCCTATGGCTGGCATATGGGCCGCAGAAGTGCGCAACAAAACAAGCAAGATGAAGCCAACCGCtt               >  1:3919960/1‑71 (MQ=255)
                                                 gCCGCTGCCTATGGCTGGCATATGGGCCGCAGAAGTGCGCAACAAAACAAGCAAGATGAAGCCAACCGCtt               >  1:2488766/1‑71 (MQ=255)
                                                 gCCGCTGCCTATGGCTGGCATATGGGCCGCAGAAGTGCGCAACAAAACAAGCAAGATGAAGCCAACCGCtt               >  1:930994/1‑71 (MQ=255)
                                                 gCCGCTGCCTATGGCTGGCATATGGGCCGCAGAAGTGCGCAACAAAACAAGCAAGATGAAGCCAACCGCtt               >  1:2027904/1‑71 (MQ=255)
                                                 gCCGCTGCCTATGGCTGGCATATGGGCCGCAGAAGTGCGCAACAAAACAAGCAAGATGAAGCCAACCGCt                >  1:2393655/1‑70 (MQ=255)
                                                        ccTATGGCTGGTATATGGGCCGCAGAAGTGCGCAACAAAACAAGCAAGATGAAGCCAACCGCTTGTcgc          <  1:3593686/69‑1 (MQ=255)
                                                        ccTATGGCTGGTATATGGGCCGCAGAAGTGCGCAACAAAACAAGCAAGATGAAGCCAACCGCTTGTcgc          <  1:2790783/69‑1 (MQ=255)
                                                        ccTATGGCTGGTATATGGGCCGCAGAAGTGCGCAACAAAACAAGCAAGATGAAGCCAACCGCTTGTCGCGt        <  1:1445543/71‑1 (MQ=255)
                                                           aTGGCTGGTATATGGGCCGCAGAAGTGCGCaacaaa                                        >  1:1137688/1‑36 (MQ=255)
                                                            tggctggcATATGGGCCGCAGAAGTGCGCaacaaaa                                       >  1:2509886/1‑36 (MQ=255)
                                                             ggCTGGTATATGGGCCGCAGAAGTGCGCAACAAAACAAGCAAGATGAAGCCAACCGCTTGTCGCGTGAtt    >  1:2383192/1‑70 (MQ=255)
                                                             ggCTGGTATATGGGCCGCAGAAGTGCGCAACAAAACAAGCAAGATGAAGCCAACCGCTTGTCGCGTGATTa   >  1:2563430/1‑71 (MQ=255)
                                                              gCTGGCATATGGGCCGCAGAAGTGCGCAACAAAACAAGCAAGATGAAGCCAACCGCTTGTCGCGTGATTAc  <  1:1529127/71‑1 (MQ=255)
                                                                   |                                                                 
GAAGGAATAACTTTCTATGCTGGAGTTGTTGTTTCTGCTTTTGCCTGTAGCCGCTGCCTATGGCTGGTATATGGGCCGCAGAAGTGCGCAACAAAACAAGCAAGATGAAGCCAACCGCTTGTCGCGTGATTAC  >  minE/879496‑879628

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