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 F17 I0 R1 87 56.5 4283937 98.6% 4223961 62.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 3,915,241 A→G 15.0% E48G (GAG→GGG)  glyQ → glycine tRNA synthetase, alpha subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,915,2410AG15.0% 146.4 / 19.4 60E48G (GAG→GGG) glyQglycine tRNA synthetase, alpha subunit
Reads supporting (aligned to +/- strand):  ref base A (22/29);  new base G (5/4);  total (27/33)
Fisher's exact test for biased strand distribution p-value = 7.18e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.29e-01

CCATTGTTCAACCATTGGACATGGAAGTCGGCGCGGGAACCTCTCACCCAATGACCTGTCTGCGCGAGCTGGGGCCAGAACCGATGGCGGCTGCTTATGTTCAGCCTTCTCGTCGCCCGACCGATGGTCGCTAC  >  W3110S.gb/3915175‑3915308
                                                                  |                                                                   
ccATTGTTCCACCATTGGACATGGAAGTCGGCGCGGGAACCTCTCACCCAATGACCTGTCTGCGCGGGCTg                                                                 >  1:2915615/1‑71 (MQ=255)
  aTTGTTCAACCATTGGACATGGAAGTCGGCGCGGGAACCTCTCACCCAATGACCTGTCTGCGCGAGCTggg                                                               <  1:3905994/71‑1 (MQ=255)
        cAACCATTGGACATGGAAGTCGGCGCGGGAACCTCTCACCCAATGCCCTGTCTGCGCGAGCTGGGGCCa                                                           >  1:2434627/1‑69 (MQ=255)
        cAACCATTGGACATGGAAGTCGGCGCGGGAACCTCTCACCCAATGACCTGTCTGCGCGAGCTGGGGCCAg                                                          >  1:3862122/1‑70 (MQ=255)
             aTTGGACATGGAAGTCGGCGCTGGAACCTCTCACCCAATGACCTGTCTGCGCGAGCTGGGGCCAGAACCGa                                                    <  1:1007297/71‑1 (MQ=255)
             aTTGGACATGGAAGTCGGCGCGGGAACCTCTCACCCAATGACCTGTCTGCGCGAGCTGGGGCCAGAACCGa                                                    <  1:1053096/71‑1 (MQ=255)
               tGGACATGGAAGTCGGCGCGGGAACCTCTCACCCAATGACCTGTCTGCGCGAGCTGGGGCCAGAACCGATg                                                  >  1:640005/1‑71 (MQ=255)
                ggACATGGAAGTCGGCGCGGGAACCTCTCACCCAATGACCTGTCTGCGCGAGCTGGGGCCAGAACCGATgg                                                 >  1:2645522/1‑71 (MQ=255)
                 gACATGGAAGTCGGCGCGGGAACCTCTCACCCAATGACCTGTCTGCGCGGGCTGGGGCCAGAACCGATggc                                                <  1:2313306/71‑1 (MQ=255)
                  aCATGGAAGTCGGCGCGGGAACCTCTCACCCAATGACCTGTCTGCGCGGGCTg                                                                 <  1:3433452/53‑1 (MQ=255)
                  aCATGGAAGTCGGCGCGGGAACCTCTCACCCAATGACCTGTCTGCGCGAGCTGGGGCCAGAACCGATggcg                                               <  1:2083083/71‑1 (MQ=255)
                  aCATGGAAGTCGGCGCGGGAACCTCTCACCCAATGACCTGTCTGCGCGAGCTGGGGCCAGAACCGATggc                                                <  1:436350/70‑1 (MQ=255)
                    aTGGAAGTCGGCGCGGGAACCTCTCACCCAATGACCTGTCTGCGCGAGCTg                                                                 <  1:4224124/51‑1 (MQ=255)
                     tGGAAGTCGGCGCGGGAACCTCTCACCCAATGACCTGTCTGCGCGAGCt                                                                  <  1:2799812/49‑1 (MQ=255)
                      ggAAGTCGGCGCGGGAACCTCTCACCCAATGACCTGTCTGCGCGGGCTGGGGCCAGAACCGATGGCGgctg                                           >  1:2229075/1‑71 (MQ=255)
                        aaGTCGGCGCGGGAACCTCTCACCCAATGACCTGTCTGCGCGGGCTGGGGCCAGAACCGATGGCGgctgct                                         >  1:3964239/1‑71 (MQ=255)
                        aaGTCGGCGCGGGAACCTCTCACCCAATGACCTGTCTGCGCGATCTGGGGCCAGAACCGATGGCGgctgct                                         <  1:1836558/71‑1 (MQ=255)
                         aGTCGGCGCGGGAACCTCTCACCCAATGACCTGTCTGCGCGAGCTGGGGCCAGAACCGATggcg                                               <  1:4192648/64‑1 (MQ=255)
                           tCGGCGCGGGAACCTCTCACCCAATGACCTGTCTGCGCGAGCTGGGGCCAGAACCGATGGCGGCTGCTTa                                       <  1:832959/70‑1 (MQ=255)
                           tCGGCGCGGGAACCTCTCACCCAATGACCTGTCTGCGCGAGCTGGGGCCAGAACCGATGGCGGCTGCTTAt                                      <  1:2826999/71‑1 (MQ=255)
                             ggCGCGGGAACCTCTCACCCAATGACCTGTCTGCGCGAGCTGGGGCCAGAAcc                                                      <  1:1350061/53‑1 (MQ=255)
                             ggCGCGGGAACCTCTCACCCAATGACCTGTCTGCGCGAGCTGGGGCCAGAACCGATGGCGGCTGCTTATg                                     <  1:2058437/70‑1 (MQ=255)
                             ggCGCGGGAACCTCTCACCCAATGACCTGTCTGCGCGAGCTGGGGCCAGAACCGATGGCGGCTGCTTATGt                                    <  1:1000782/71‑1 (MQ=255)
                              gcgcGGGAACCTCTCACCCAATGACCTGTCTGCGCGAGCTGGGGCCAGAACCGATGGCGGCTGCTTATGtt                                   <  1:2739882/71‑1 (MQ=255)
                               cgcgGGAACCTCTCACCCAATGACCTGTCTGAGCGAGCTGGGGCCAGAACCGATGGCGGCTGCTTATGTTc                                  <  1:3572137/71‑1 (MQ=255)
                               cgagggAACCTCTCACCCAATGACCTGTCTGCGCGAGCTGGGGCCAGAACCGATGGCGGCTGCTTATGTTc                                  <  1:3235307/68‑1 (MQ=255)
                                   ggAACCTCTCACCCAATGACCTGTCTGCGCGAGCTg                                                                 <  1:2496556/36‑1 (MQ=255)
                                      aCCTCTCACCCAATGACCTGTCTGCGCGAGCTGGGGCCAGAACCGATggcg                                               >  1:800158/1‑51 (MQ=255)
                                      aCCTCTCACCCAATGACCTGTCTGCGCGAGCTGGGGCCAGAACCGATGGCGGCTGCTTATGTTCAGCCtt                            <  1:924614/70‑1 (MQ=255)
                                        ctctCACCCAATGACCTGTCTGCGCGGGCTGGGGCCAGAAcc                                                      <  1:1596093/42‑1 (MQ=255)
                                        ctctCACCCAATGACCTGTCTGCGCGAGCTGGGGCCAGAACCGATGGCGGCTGCTTATGTTCAGCCTtctc                         >  1:3333055/1‑71 (MQ=255)
                                         tctcACCCAATGACCTGTCTGCGCGGGCTGGGGCCAGAACCGATGGCGGCTGCTTATGTTCAGCCTTCtcg                        >  1:1937859/1‑71 (MQ=255)
                                           tcACCCAATGACCTGTCTGCGCGGGCTGGGGCCAGAACCGATGGCGGCTGCTTATGTTCAGCCTTCtcgtc                      >  1:2451494/1‑71 (MQ=255)
                                           tcACCCAATGACCTGTCTGCGCGGGCTGGGGCCAGAACCGATGGCGGCTGCTTATGTTCAGCCTTCtcg                        <  1:306310/69‑1 (MQ=255)
                                           tcACCCAATGACCTGTCTGCGCGAGCTGGGGCCAGAACCGATGGCGgctgc                                          >  1:3379636/1‑51 (MQ=255)
                                            cACCCAATGACCTGTCTGCGCGAGCTGGGGCCAGAACCGATGGCGGCTGCTTATGtt                                   <  1:4162671/57‑1 (MQ=255)
                                               ccAATGACCTGTCTGCGCGAGCTGGGGCCAGAACCGATggcggc                                             <  1:3913514/44‑1 (MQ=255)
                                                cAATGACCTGTCTGCGCGAGCTGGGGCCAGAACCGATGGCGGCTGCTTATGTTCAGCCTTCTCGTCGCccg                 <  1:834271/71‑1 (MQ=255)
                                                cAATGACCTGTCTGCGCGAGCTGGGGCCAGAACCGATGGCGGCTGCTTATGTTCAGCCTTCTCGTCGCccg                 <  1:584946/71‑1 (MQ=255)
                                                 aaTGACCTGTCTGCGCGAGCTGGGGCCAGAACCGATGGCGGCTGCTTATGTTCAGCCTTCtcgtc                      >  1:652071/1‑65 (MQ=255)
                                                  aTGACCTGTCTGCGCGAGCTGGGGCCAGAACCGATGGCGGCTGCTTATGtt                                   >  1:2481222/1‑51 (MQ=255)
                                                  aTGACCTGTCTGCGCGAGCTGGGGCCAGAACCGATGGCGGCTGCTTATGTTCAGCCtt                            <  1:935762/58‑1 (MQ=255)
                                                  aTGACCTGTCTGCGCGAGCTGGGGCCAGAACCGATGGCGGCTGCTTATGTTCAGCCTTCTCGTCGCccgac               >  1:2609198/1‑71 (MQ=255)
                                                  aTGACCTGTCTGCGCGAGCTGGGGCCAGAACCGATGGCGGCTGCTTATGTTCAGCCTTCTCGTCGCccgac               <  1:738403/71‑1 (MQ=255)
                                                  aTGACCTGTCTGCGCGAGCTGGGGCCAGAACCGATGGCGGCTGCTTATGTTCAGCCTTCTCGTCGCccgac               >  1:686315/1‑71 (MQ=255)
                                                   tGACCTGTCTGCGCGATCTGGGGCCAGAACCGATGGCGGCTGCTTATGTTCAGCCTTCTCGTCGCccgacc              <  1:798039/71‑1 (MQ=255)
                                                   tGACCTGTCTGCGCGAGCTGGGGCCAGAACCGATGGCGGCTGCTTATGTTCAGCCTTCTCGTCGCccgacc              >  1:716848/1‑71 (MQ=255)
                                                     aCCTGTCTGCGCGAGCTGGGGCCAGAACCGATGGCGGCTGCTTATGTTCAGCCTTCTCGTCGCccgaccga            >  1:3678861/1‑71 (MQ=255)
                                                     aCCTGTCTGCGCGAGCTGGGGCCAGAACCGATGGCGGCTGCTTATGTTCAGCCTTCTCGTCGCccgaccga            >  1:3421892/1‑71 (MQ=255)
                                                      ccTGTCTGCGCGAGCTGGGGCCAGAACCGATGGCGGCTGCTTATGTTCAGCCTTCTCGTCGCccgaccga            <  1:3303709/70‑1 (MQ=255)
                                                         gTCTGCGCGAGCTGGGGCCAGAACCGATGGCGGCTGCTTATGTTCAGCCTTCTCGTCGCCCGACCGAt           <  1:2064304/68‑1 (MQ=255)
                                                          tCTGCGCGAGCTGGGGCCAGAACCGATGGCGGCTGCTTATGTTCAGCCTTCTCGTCGCCCGACCGATGGTc       >  1:3030832/1‑71 (MQ=255)
                                                            tGCGCGAGCTGGGGCCAGAACCGATGGCGGCTGCTTAt                                      >  1:2691296/1‑38 (MQ=255)
                                                            tGCGCGAGCTGGGGCCAGAACCGATGGCGGCTGCTTATGTTCAGcc                              >  1:2497770/1‑46 (MQ=255)
                                                            tGCGCGAGCTGGGGCCAGAACCGATGGCGGCTGCTTATGTTCAGcc                              >  1:1667434/1‑46 (MQ=255)
                                                            tGCGCGAGCTGGGGCCAGAACCGATGGCGGCTGCTTATGTTCAGCCTtctc                         >  1:3247575/1‑51 (MQ=255)
                                                            tGCGCGAGCTGGGGCCAGAACCGATGGCGGCTGCTTATGTTCAGCCTTCTCGTCGCCCGACCGATGGTCGc     >  1:2778437/1‑71 (MQ=255)
                                                              cgcgAGCTGGGGCCAGAACCGATGGCGTCTGCTTATGTTCAGCCTTCTCGTCGCCCGACCGATGGTCGc     >  1:1494048/1‑69 (MQ=255)
                                                               gcgAGCTGGGGCCAGAACCGATGGCGGCTGCTTATGTTCAGCCTTCTCGTCGCccgaccga            >  1:1923806/1‑61 (MQ=255)
                                                               gcgAGCTGGGGCCAGAACCGATGGCGGCTGCTTATGTTCAGCCTTCTCGTCGCCCGACCGATGGTCGCTAc  <  1:1432040/71‑1 (MQ=255)
                                                                  |                                                                   
CCATTGTTCAACCATTGGACATGGAAGTCGGCGCGGGAACCTCTCACCCAATGACCTGTCTGCGCGAGCTGGGGCCAGAACCGATGGCGGCTGCTTATGTTCAGCCTTCTCGTCGCCCGACCGATGGTCGCTAC  >  W3110S.gb/3915175‑3915308

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