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
A6 F21 I0 R1 2169 63.0 3952800 76.2% 3012033 62.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,789,192 T→C 34.2% V110A (GTG→GCG)  ygaF → hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,789,1920TC34.2% 75.7 / 69.0 76V110A (GTG→GCG) ygaFhypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (26/24);  new base C (12/14);  total (38/38)
Fisher's exact test for biased strand distribution p-value = 8.09e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.34e-01

CGGCAAGATGCTGGTTGCCACGTCCGATCTCGAAATGGAACGGATGCGCGCCTTATGGGAACGCACAGTGGCGAACGGTATCGAGCGCGAATGGCTTAACGCCGACGAACTGCGCGAGCGCGAACCGAATATCAC  >  minE/1789124‑1789258
                                                                    |                                                                  
cGGCAAGATGCTGGTTGCCTCGTGCGATCTCGAAATGGAACGGATGCGCGCCTTATGGGAACGCACAGt                                                                    <  1:1100438/69‑1 (MQ=255)
cGGCAAGATGCTGGTTGCCACGTCCGATCTCGAAATGGAACGGATGCGCGCCTTATGGGAACGCACAGt                                                                    <  1:3444538/69‑1 (MQ=255)
cGGCAAGATGCTGGTTGCCACGTCCGATCTCGAAATGGAACGGATGCGCGCCTTATGGGAACGCACAGTg                                                                   <  1:2855954/70‑1 (MQ=255)
 ggCAAGATGCTGGTTGCCACGTCCGATCTCGAAATGGAACGGATGCGCGCCTTATGGGAACGCACAGt                                                                    <  1:2800521/68‑1 (MQ=255)
 ggCAAGATGCTGGTTGCCACGTCCGATCTCGAAATGGAACGGATGCGCGCCTTATGGGAACGCACAGTGGc                                                                 >  1:2708294/1‑71 (MQ=255)
 ggCAAGATGCTGGTTGCCACGTCCGATCTCGAAATGGAACGGATGCGCGCCTTATGGGAACGCACAGTGGc                                                                 >  1:902220/1‑71 (MQ=255)
 ggCAAGATGCTGGTTGCCACGTCCGATCTCGAAATGGAACGGATGCGCGCCTTATGGGAACGCACAGCGGc                                                                 <  1:906638/71‑1 (MQ=255)
  gCAAGATGCTGGTTGCCACGTCCGATCTCGAAATGGAACGGATGCGCGCCTTATGGGAACGCACAGTGGCg                                                                <  1:142169/71‑1 (MQ=255)
  gCAAGATGCTGGTTGCCACGTCCGATCTCGAAATGGAACGGATGCGCGCCTTATGGGAACGCACAGTGGCg                                                                <  1:137600/71‑1 (MQ=255)
       aTGCTGGTTGCCACGTCCGATCTCGAAATGGAACGGATGCGCGCCTTATGGGAACGCACAGCGGCGAACgg                                                           >  1:3796821/1‑71 (MQ=255)
        tGCTGGTTGCCACGTCCGATCTCGAAATGGAACGGATGCGCGCCTTATGGGAACGCACAGTGGc                                                                 >  1:700694/1‑64 (MQ=255)
        tGCTGGTTGCCACGTCCGATCTCGAAATGGAACGGATGCGCGCCTTATGGGAACGCACAGCGGCGAACGGt                                                          <  1:3448518/71‑1 (MQ=255)
          cTGGTTGCCACGTCCGATCTCGAAATGGAACGGATGCGCGCCTTATGGGAACGCACAGTGGCGAACGGTAt                                                        >  1:2013095/1‑71 (MQ=255)
           tGGTTGCCACGTCCGATCTCGAAATGGAACGGATGCGCGCCTTATGGGAACGCACAGTGGCGAACGGTATc                                                       >  1:3636781/1‑71 (MQ=255)
           tGGTTGCCACGTCCGATCTCGAAATGGAACGGATGCGCGCCTTATGGGAACGCACAGCgg                                                                  >  1:1445830/1‑60 (MQ=255)
              ttGCCACGTCCGATCTCGAAATGGAACGGATGCGCGCCTTATGGGAACGCACAGTGGCGAACGGTATCGAg                                                    >  1:381154/1‑71 (MQ=255)
               tGCCACGTCCGATCTCGAAATGGAACGGATGCGCGCCTTATGGGAACGCACAGTg                                                                   >  1:1214493/1‑55 (MQ=255)
               tGCCACGTCCGATCTCGAAATGGAACGGATGCGCGCCTTATGGGAACGCACAGTg                                                                   >  1:2734812/1‑55 (MQ=255)
                gCCACGTCCGATCTCGAAATGGAACGGATGCGCGCCTTATGGGAACGCACAGTGGCGAACGGTa                                                         >  1:2306516/1‑64 (MQ=255)
                gCCACGTCCGATCTCGAAATGGAACGGATGCGCGCCTTATGGGAACGCACAGTGGCGAACGGTa                                                         >  1:1488787/1‑64 (MQ=255)
                gCCACGTCCGATCTCGAAATGGAACGGATGCGCGCCTTATGGGAACGCACAGTGGCGAACGGTATCGAgcg                                                  >  1:2056029/1‑71 (MQ=255)
                gCCACGTCCGATCTCGAAATGGAACGGATGCGCGCCTTATGGGAACGCACAGTGGCGAACGGTATCGAgc                                                   <  1:3210648/70‑1 (MQ=255)
                gCCACGTCCGATCTCGAAATGGAACGGATGCGCGCCTTATGGGAACGCACAGTGGCGAACGGTATCGAgc                                                   <  1:2989182/70‑1 (MQ=255)
                gCCACGTCCGATCTCGAAATGGAACGGATGCGCGCCTTATGGGAACGCACAGTGGCGAACGGTATCGAgc                                                   <  1:324149/70‑1 (MQ=255)
                  cACGTCCGATCTCGAAATGGAACGGATGCGCGCCTTATGGGAACGCACAGTGGCGAACGGTATCGAgcgc                                                 >  1:3788578/1‑70 (MQ=255)
                  cACGTCCGATCTCGAAATGGAACGGATGCGCGCCTTATGGGAACGCACAGTGGCGAACGGTATCGAgcgc                                                 >  1:3415553/1‑70 (MQ=255)
                   aCGTCCGATCTCGAAATGGAACGGATGCGCGCCTTATGGGAACGCACAGCGGCGAACGGTa                                                         >  1:1133937/1‑61 (MQ=255)
                   aCGTCCGATCTCGAAATGGAACGGATGCGCGCCTTATGGGAACGCACAGCGGCGAACGGTATCGAGCGCGa                                               <  1:1780554/71‑1 (MQ=255)
                      tCCGATCTCGAAATGGAACGGATGCGCGCCTTATGGGAACGCACAGCGGCGAACGGTATCGAGCGCGAATg                                            >  1:863700/1‑71 (MQ=255)
                         gATCTCGAAATGGAACGGATGCGCGCCTTATGGGAACGCACAGTGGCGAACGGTATCGAGcgcg                                                <  1:1807161/64‑1 (MQ=255)
                          aTCTCGAAATGGAACGGATGCGCGCCTTATGGGAACGCACAGTGGCg                                                                <  1:2794878/47‑1 (MQ=255)
                           tctcGAAATGGAACGGATGCGCGCCTTATGGGAACGCACAGTGGCGAACGGTATCGAGCGCGaa                                              >  1:48141/1‑64 (MQ=255)
                           tctcGAAATGGAACGGATGCGCGCCTTATGGGAACGCACAGCGGCGAACGGTATCGAGCGCGAATGGCtt                                        >  1:723141/1‑70 (MQ=255)
                           tctcGAAATGGAACGGATGCGCGCCTTATGGGAACGCACAGCGGCGAACGGTATCGAGCGCGAATGGCt                                         >  1:2843567/1‑69 (MQ=255)
                               gAAATGGAACGGATGCGCGCCTTATGGGAACGCATAGCGGCGAACGGTATCGAGCGCGAATGGCt                                         <  1:2854749/65‑1 (MQ=255)
                               gAAATGGAACGGATGCGCGCCTTATGGGAACGCACAGTGGCGAACGGTATCGAGCGCTAAt                                             <  1:65754/61‑1 (MQ=255)
                               gAAATGGAACGGATGCGCGCCTTATGGGAACGCACAGTGGCGAACGGTATCGAGCGCGAAt                                             <  1:3768256/61‑1 (MQ=255)
                               gAAATGGAACGGATGCGCGCCTTATGGGAACGCACAGTGGCGAACGGTATCGAGCGCGAAt                                             <  1:3703357/61‑1 (MQ=255)
                               gAAATGGAACGGATGCGCGCCTTATGGGAACGCACAGCGGCGAACGGTATCGAGCGCGAATGGCt                                         <  1:198519/65‑1 (MQ=255)
                               gAAATGGAACGGATGCGCGCCTTATGGGAACGCACAGCGGCGAACGGTATCGAGCGCGAATGGCTTa                                       <  1:453067/67‑1 (MQ=255)
                                aaaTGGAACGGATGCGCGCCTTATGGGAACGCACAGTGGCGAAc                                                             >  1:1367648/1‑44 (MQ=255)
                                 aaTGGAACGGATGCGCGCCTTATGGGAACGCACAGTGGCGAACGGTATCGAGCGCGAATGGCTTAACGCcg                                 <  1:3767245/71‑1 (MQ=255)
                                 aaTGGAACGGATGCGCGCCTTATGGGAACGCACAGCGGCGAACGGTATCGAGCGCCAATGGCTTAACGcc                                  >  1:2976728/1‑70 (MQ=255)
                                  aTGGAACGGATGCGCGCCTTATGGGAACGCACAGCGGCGAACGGTATCGAGCGCGa                                               <  1:1626860/56‑1 (MQ=255)
                                  aTGGAACGGATGCGCGCCTTATGGGAACGCACAGCGGCGAACGGTATCGAGCGCGa                                               <  1:1390367/56‑1 (MQ=255)
                                  aTGGAACGGATGCGCGCCTTATGGGAACGCACAGCGGCGAACGGTATCGAGCGCGAATGGCTTAACGCcga                                >  1:3533278/1‑71 (MQ=255)
                                    ggAACGGATGCGCGCCTTATGGGAACGCACAGTGGCGAACGGTATCGAGcgcg                                                >  1:3737609/1‑53 (MQ=255)
                                     gAACGGATGCGCGCCTTATGGGAACGCACAGTGGCGAACGGTATCGAGcgcg                                                <  1:1086739/52‑1 (MQ=255)
                                     gAACGGATGCGCGCCTTATGGGAACGCACAGTGGCGAACGGTATCGAGCGCGAATGGCTTAACGCcgacg                              <  1:3601643/70‑1 (MQ=255)
                                     gAACGGATGCGCGCCTTATGGGAACGCACAGCGGCGAACGGTATCGAGCGCGAATGGCTTAACGCcgacg                              >  1:3710466/1‑70 (MQ=255)
                                     gAACGGATGCGCGCCTTATGGGAACGCACAGCGGCGAACGGTATCGAGCGCGAATGGCTTAACGCcgacg                              <  1:1523242/70‑1 (MQ=255)
                                            tGCGCGCCTTATGGGAACGCACAGCGGCGAACGGTATCGAGCGCGAATGGCTTAACGCCGACGAACTgcgc                      <  1:856146/71‑1 (MQ=255)
                                              cgcgcCTTATGGGAACGCACAGTGGCGAACGGTATCGAGCGCGAATGGCTTAACGCCGACGAACTgcgcga                    <  1:2974554/71‑1 (MQ=255)
                                              cgcgcCTTATGGGAACGCACAGTGGCGAACGGTATCGAGCGCGAATGGCTTAACGCCGACGAACTgcgcg                     <  1:965235/70‑1 (MQ=255)
                                                 gcCTTATGGGAACGCACAGTGGCGAACGGTATCGAGCGCGAATAGCTTaa                                      <  1:863116/50‑1 (MQ=255)
                                                  ccTTATGGGAACGCACAGCGGCGAACGGTATCGAGCGCGAATGGCTTAACGCCGACGAACTgcgcgagcgc                <  1:2812349/71‑1 (MQ=255)
                                                   cTTATGGGAACGCACAGTGGCGAACGGTATCGAGcgcg                                                <  1:3276249/38‑1 (MQ=255)
                                                   cTTATGGGAACGCACAGTGGCGAACGGTATCGAGcgcg                                                <  1:2738011/38‑1 (MQ=255)
                                                   cTTATGGGAACGCACAGTGGCGAACGGTATCGAGCGCGAATGGCTTa                                       <  1:2067930/47‑1 (MQ=255)
                                                   cTTATGGGAACGCACAGCGGCGAACGGTATCGAGCGCGAATg                                            <  1:3576239/42‑1 (MQ=255)
                                                   cTTATGGGAACGCACAGCGGCGAACGGTATCGAGCGCGAATg                                            <  1:2356609/42‑1 (MQ=255)
                                                   cTTATGGGAACGCACAGCGGCGAACGGTATCGAGCGCGAATg                                            <  1:158141/42‑1 (MQ=255)
                                                    ttATGGGAACGCACAGTGGCGAACGGTATCGAGCGCGAAt                                             >  1:1864792/1‑40 (MQ=255)
                                                    ttATGGGAACGCACAGCGGCGAACGGTATCGAGCGCGAATGGCTTAACGCCGACGAACTgcgcgagcgcg               >  1:1337531/1‑70 (MQ=255)
                                                    ttATGGGAACGCACAGCGGCGAACGGTATCGAGCGCGAATGGCTTAACGCCGACGAACTgcgcgagcgcg               >  1:149127/1‑70 (MQ=255)
                                                      aTGGGAACGCACAGTGGCGAACGGTATCGAGCGCGAATGGCTTAACGCCGACGAACTgcgcgagcgcga              <  1:1270239/69‑1 (MQ=255)
                                                      aTGGGAACGCACAGTGGCGAACGGTATCGAGCGCGAATGGCTTAACGCCGACGAACTgcgcgagcgcga              <  1:1599548/69‑1 (MQ=255)
                                                        gggAACGCACAGCGGCGAACGGTATCGAGCGCGAATGGCTTAACg                                    >  1:1035178/1‑45 (MQ=255)
                                                         ggAACGCACAGTGGCGAACGGTATCGAGCGCGAATGGCTTAACGCCGACGAACTGCGCGAGCGCGAACCg          <  1:1240400/70‑1 (MQ=255)
                                                          gAACGCACAGTGGCGAACGGTATCGAGCGCGAATGGCTTAACGCCGACGAACTgcgcgagcgcg               >  1:1925400/1‑64 (MQ=255)
                                                          gAACGCACAGTGGCGAACGGTATCGAGCGCGAATGGCTTAACGCCGACGAACTGCGCGAGCGCGAACCGa         >  1:3854585/1‑70 (MQ=255)
                                                            aCGCACAGTGGCGAACGGTATCGAGCGCGAATGGCTTAACGCCGACGAACTGCGCGAGCGCGAACCGAata      >  1:1873076/1‑71 (MQ=255)
                                                             cGCACAGTGGCGAACGGTATCGAGCGCGAATGGCTTAACGCCGACGAACTGCGCGAGCGCGAACCGAatat     >  1:3179767/1‑71 (MQ=255)
                                                                acaGTGGCGAACGGTATCGAGCGCGAATGGCTTAACGCCGACGAACTGCGCGAGCGCGAACCGAATATCAc  >  1:529529/1‑71 (MQ=255)
                                                                acaGTGGCGAACGGTATCGAGCGCGAATGGCTTAACGCCGACGAACTGCGCGAGCGCGAACCGAATATCAc  >  1:1321713/1‑71 (MQ=255)
                                                                acaGTGGCGAACGGTATCGAGCGCGAATGGCTTAACGCCGACGAACTGCGCGAGCGCGAACCGAATATCAc  >  1:1043004/1‑71 (MQ=255)
                                                                  aGTGGCGAACGGTATCGAGCGCGAATGGCTTAACGCCGCCGAACTGCGCGAGCGCGAACCGAat       >  1:301855/1‑64 (MQ=255)
                                                                  aGTGGCGAACGGTATCGAGCGCGAATGGCTTAACGCCGACGAACTGCGCGAGCGCGAACCGAat       >  1:1629235/1‑64 (MQ=255)
                                                                   gTGGCGAACGGTATCGAGCGCGAATGGCTTAACGCcgacg                              <  1:3782657/40‑1 (MQ=255)
                                                                    tGGCGAACGGTATCGAGCGCGAATGCCTTAACGCcgacga                             >  1:827025/1‑40 (MQ=255)
                                                                    |                                                                  
CGGCAAGATGCTGGTTGCCACGTCCGATCTCGAAATGGAACGGATGCGCGCCTTATGGGAACGCACAGTGGCGAACGGTATCGAGCGCGAATGGCTTAACGCCGACGAACTGCGCGAGCGCGAACCGAATATCAC  >  minE/1789124‑1789258

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