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 F28 I1 R1 163 52.9 1786516 99.3% 1774010 139.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,606,467 T→C V69A (GTG→GCG)  hyfE → hydrogenase 4 component E

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,606,4670TC97.7% 144.4 / ‑4.9 43V69A (GTG→GCG) hyfEhydrogenase 4 component E
Reads supporting (aligned to +/- strand):  ref base T (1/0);  new base C (20/22);  total (21/22)
Fisher's exact test for biased strand distribution p-value = 4.88e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

TCAAAAGCTATCGCCTGTCATGCGGATTTTACGCCTGCCAGTCACTGGTGCTGGTGTCTATTTTCGCCACTCTCTCGTGCCTGTTCGCCGCAGAGCAACTGCTGATCTGGTCCGCCAGCGCCTTTATCACCAAAGTGCTGCTGGTACCGTTAATCATGACTTACGCTGCACGAAATATTCCCCAGAACATCCCGGAAAAAGCGTTATTCGGTCCGGCAATGATGGCACTGCTCGCGGCGTTAATTGTCCTGCTTTGCGCATTTGTCGTTC  >  NC_000913/2606332‑2606601
                                                                                                                                       |                                                                                                                                      
tCAAAAGCTATCGCCTGTCATGCGGATTTTACGCCTGCCAGTCACTGGTGCTGGTGTCTA‑TTTCGCCACTCTCTCGTGCCTGTTCGCCGCAGAGCAACTGCTGATCTGGTCCGCCAGCGCCTTTATCACCAAAGcgctgc                                                                                                                                   <  2:828531/140‑1 (MQ=255)
 cAAAAGCTATCGCCTGTCATGCGGATTTTACGCCTGCCAGTCACTGGTGCTGGTGTCTATTTTCGCCACTCTCTCGTGCCTGTTCGCCGCAGAGCAACTGCTGATCTGGTCCGCCAGCGCCTTTATCACCAAAGcgctgc                                                                                                                                   >  2:344536/1‑140 (MQ=255)
   aaaGCTATCGCCTGTCATGCGGATTTTACGCCTGCCAGTCACTGGTGCTGGTGTCTATTTTCGCCACTCTCTCGTGCCTGTTCGCCGCAGAGCAACTGCTGATCTGGTCCGCCAGCGCCTTTATCACCAAAGCGctgctg                                                                                                                                 >  1:874312/1‑140 (MQ=255)
   aaaGCTATCGCCTGTCATGCGGATTTTACGCCTGCCAGTCACTGGTGCTGGTGTCTATTTTCGCCACTCTCTCGTGCATGTTCGCCGCAGAGCAACTGCTGATCTGGTCCGCCAGCGCCTTTATCACCAAAGCGctgctg                                                                                                                                 <  2:796577/140‑1 (MQ=255)
     aGCTATCGCCTGTCATGCGGATTTTACGCCTGCCAGTCACTGGTGCTGGTGTCTATTTTCGCCACTCTCTCGTGCCTGTTCGCCGCAGAGCAACTGCTGATCTGGTCCGCCAGCGCCTTTATCACCAAAGCGCTGCTGGt                                                                                                                               <  2:143341/140‑1 (MQ=255)
          tCGCCTGTCATGCGGATTTTACGCCTGCCAGTCACTGGTGCTGGTGTCTATTTTCGCCACTCTCTCGTGCCTGTTCGCCGCAGAGCAACTGCTGATCTGGTCCGCCAGCGCCTTTATCACCAAAGCGCTGCTGGTACCGt                                                                                                                          >  2:384763/1‑140 (MQ=255)
                gTCATGCGGATTTTACGCCTGCCAGTCACTGGTGCTGGTGTCTATTTTCGCCACTCTCTCGTGCCTGTTCGCCGCAGAGCAACTGCTGATCTGGTCCGCCAGCGCCTTTATCACCAAAGCGCTGCTGGTACCGTTAATCa                                                                                                                    >  1:357917/1‑140 (MQ=255)
                 tCATGCGGATTTTACGCCTGCCAGTCACTGGTGCTGGTGTCTATTTTCGCCACTCTCTCGTGCCTGTTCGCCGCAGAGCAACTGCTGATCTGGTCCGCCAGCGCCTTTATCACCAAAGCGCTGCTGGTACCGTTAATc                                                                                                                     >  1:291853/1‑138 (MQ=255)
                 tCATGCGGATTTTACGCCTGCCAGTCACTGGTGCTGGTGTCTATTTTCGCCACTCTCTCGTGCCTGTTCGCCGCAGAGCAACTGCTGATCTGGTCCGCCAGCGCCTTTATCACCAAAGCGCTGCTGGTACCGTTAATc                                                                                                                     <  2:291853/138‑1 (MQ=255)
                 tCATGCGGATTTTACGCCTGCCAGTCACTGGTGCTGGTGTCTATTTTCGCCACTCTCTCGTGCCTGTTCGCCGCAGAGCAACTGCTGATCTGGTCCGCCAGCGCCTTTATCACCAAAGCGCTGCTGGTACCGTTAATCAt                                                                                                                   <  2:824070/140‑1 (MQ=255)
                    tGCGGATTTTACGCCTGCCAGTCACTGGTGCTGGTGTCTATTTTCGCCACTCTCTCGTGCCTGTTCGCCGCAGAGCAACTGCTGATCTGGTCCGCCAGCGCCTTTATCACCAAAGCGCTGCTGGTACCGTTAATCATGAc                                                                                                                >  1:459687/1‑140 (MQ=255)
                    tGCGGATTTTACGCCTGCCAGTCACTGGTGCTGGTGTCTATTTTCGCCACTCTCTCGTGCCTGTTCGCCGCAGAGCAACTGCTGATCTGGTCCGCCAGCGCCTTTATCACCAAAGCGCTGCTGGTACCGTTAATCATGAc                                                                                                                >  1:626100/1‑140 (MQ=255)
                         aTTTTACGCCTGCCAGTCACTGGTGCTGGTGTCTATTTTCGCCACTCTCTCGTGCCTGTTCGCCGCAGAGCAACTGCTGATCTGGTCCGCCAGCGCCTTTATCACCAAAGCGCTGCTGGTACCGTTAATCATGACTTACg                                                                                                           <  1:132323/140‑1 (MQ=255)
                           tttACGCCTGCCAGTCACTGGTGCTGGTGTCTATTTTCGCCACTCTCTCGTGCCTGTTCGCCGCAGAGCAACTGCTGATCTGGTCCGCCAGCGCCTTTATCACCAAAGCGCTGCTGGTACCGTTAATCATGACTTACGCt                                                                                                         >  1:591270/1‑140 (MQ=255)
                           tttACGCCTGCCAGTCACTGGTGCTGGTGTCTATTTTCGCCACTCTCTCGTGCCTGTTCGCCGCAGAGCAACTGCTGATCTGGTCCGCCAGCGCCTTTATCACCAAAGCGCTGCTGGTACCGTTAATCATGACTTACGCt                                                                                                         <  2:441322/140‑1 (MQ=255)
                             tACGCCTGCCAGTCACTGGTGCTGGTGTCTATTTTCGCCACTCTCTCGTGCCTGTTCGCCGCAGAGCAACTGCTGATCTGGTCCGCCAGCGCCTTTATCACCAAAGCGCTGCTGGTACCGTTAATCATGACTTACGCTGc                                                                                                       <  1:732228/140‑1 (MQ=255)
                              aCGCCTGCCAGTCACTGGTGCTGGTGTCTATTTTCGCCACTCTCTCGTGCCTGTTCGCCGCAGAGCAACTGCTGATCTGGTCCGCCAGCGCCTTTATCACCAAAGCGCTGCTGGTACCGTTAATCATGACTTACGCTGCa                                                                                                      <  2:874312/140‑1 (MQ=255)
                                     ccAGTCACTGGTGCTGGTGTCTATTTTCGCCACTCTCTCGTGCCTGTTCGCCGCAGAGCAACTGCTGATCTGGTCCGCCAGCGCCTTTATCACCAAAGCGCTGCTGGTACCGTTAATCATGACTTACGCTGCACGAAata                                                                                               <  2:626100/140‑1 (MQ=255)
                                     ccAGTCACTGGTGCTGGTGTCTATTTTCGCCACTCTCTCGTGCCTGTTCGCCGCAGAGCAACTGCTGATCTGGTCCGCCAGCGCCTTTATCACCAAAGCGCTGCTGGTACCGTTAATCATGACTTACGCTGCACGAAata                                                                                               <  1:689886/140‑1 (MQ=255)
                                         tCACTGGTGCTGGTGTCTATTTTCGCCACTCTCTCGTGCCTGTTCGCCGCAGAGCAACTGCTGATCTGGTCCGCCAGCGCCTTTATCACCAAAGCGCTGCTGGTACCGTTAATCATGACTTACGCTGCACGAAATATTcc                                                                                           <  2:96817/140‑1 (MQ=255)
                                                  ctggtgTCTATTTTCGCCACTCTCTCGTGCCTGTTCGCCGCAGAGCAACTGCTGATCTGGTCCGCCAGCGCCTTTATCACCAAAGCGCTGCTGGTACCGTTAATCATGACTTACGCTGCACGAAATATTCCCCAGAACAt                                                                                  >  2:218604/1‑140 (MQ=255)
                                                     gtgtCTATTTTCGCCACTCTCTCGTGCCTGTTCGCCGCAGAGCAACTGCTGATCTGGTCCGCCAGCGCCTTTATCACCAAAGCGCTGCTGGTACCGTTAATCATGACTTACGCTGCACGAAATATTCCCCAGAACATccc                                                                               >  2:575836/1‑140 (MQ=255)
                                                       gtCTATTTTCGCCACTCTCTCGTGCCTGTTCGCCGCAGAGCAACTGCTGATCTGGTCCGCCAGCGCCTTTATCACCAAAGTGCTGCTGGTACCGTTAATCATGACTTACGCTGCACGAAATATTCCCCAGAACATCCCgg                                                                             >  1:534925/1‑140 (MQ=255)
                                                       gtCTATTTTCGCCACTCTCTCGTGCCTGTTCGCCGCAGAGCAACTGCTGATCTGGTCCGCCAGCGCCTTTATCACCAAAGCGCTGCTGGTACCGTTAATCATGACTTACGCTGCACGAAATATTCCCCAGAACATCCCgg                                                                             >  1:16446/1‑140 (MQ=255)
                                                         cTATTTTCGCCACTGTCTCGTGCCTGTTCGCCGCAGAGCAACTGCTGATCTGGTCCGCCAGCGCCTTTATCACCAAAGCGCTGCTGGTACCGTTAATCATGACTTACGCTGCACGAAATATTCCCCAGAACATCCCGGaa                                                                           >  1:211167/1‑140 (MQ=255)
                                                          tATTTTCGCCACTCTCTCGTGCCTGTTCGCCGCAGAGCAACTGCTGATCTGGTCCGCCAGCGCCTTTATCACCAAAGCGCTGCTGGTACCGTTAATCATGACTTACGCTGCACGAAATATTCCCCAGAACATCCCGGaaa                                                                          <  1:67214/140‑1 (MQ=255)
                                                          tATTTTCGCCACTCTCTCGTGCCTGTTCGCCGCAGAGCAACTGCTGATCTGGTCCGCCAGCGCCTTTATCACCAAAGCGCTGCTGGTACCGTTAATCATGACTTACGCTGCACGAAATATTCCCCAGAACATCCCGGaaa                                                                          >  2:710794/1‑140 (MQ=255)
                                                                    aCTCTCTCGTGCCTGTTCGCCGCAGAGCAACTGCTGATCTGGTCCGCCAGCGCCTTTATCACCAAAGCGCTGCTGGTACCGTTAATCATGACTTACGCTGCACGAAATATTCCCCAGAACATCCCGGAAAAAGCGTTAtt                                                                <  2:357917/140‑1 (MQ=255)
                                                                    aCTCTCTCGTGCCTGTTCGCCGCAGAGCAACTGCTGATCTGGTCCGCCAGCGCCTTTATCACCAAAGCGCTGCTGGTACCGTTAATCATGACTTACGCTGCACGAAATATTCCCCAGAACATCCCGGAAAAAGCGTTAtt                                                                >  1:843841/1‑140 (MQ=255)
                                                                    aCTCTCTCGTGCCTGTTCGCCGCAGAGCAACTGCTGATCTGGTCCGCCAGCGCCTTTATCACCAAAGCGCTGCTGGTACCGTTAATCATGACTTACGCTGCACGAAATATTCCCCAGAACATCCCGGAAAAAGCGTTAtt                                                                <  2:16446/140‑1 (MQ=255)
                                                                       ctctcGTGCCTGTTCGCCGCAGAGCAACTGCTGATCTGGTCCGCCAGCGCCTTTATCACCAAAGCGCTGCTGGTACCGTTAATCATGACTTACGCTGCACGAAATATTCCCCAGAACATCCCGGAAAAAGCGTTATTCgg                                                             <  2:349131/140‑1 (MQ=255)
                                                                             tGCCTGTTCGCCGCAGAGCAACTGCTGATCTGGTCCGCCAGCGCCTTTATCACCAAAGCGCTGCTGGTACCGTTAATCATGACTTACGCTGCACGAAATATTCCCCAGAACATCCCGGAAAAAGCGTTATTCGGTCCGGc                                                       <  2:23827/140‑1 (MQ=255)
                                                                                 tGTTCGCCGCAGAGCAACTGCTGATCTGGTCCGCCAGCGCCTTTATCACCAAAGCGCTGCTGGTACCGTTAATCATGACTTACGCTGCACGAAATATTCCCCAGAACATCCCGGAAAAAGCGTTATTCGGTCCGGCAatg                                                   >  2:193334/1‑140 (MQ=255)
                                                                                  gTTCGCCGCAGAGCAACTGCTGATCTGGTCCGCCAGCGCCTTTATCACCAAAGCGCTGCTGGTACCGTTAATCATGACTTACGCTGCACGAAATATTCCCCAGAACATCCCGGAAAAAGCGTTATTCGGTCCGGCAatga                                                  >  2:626149/1‑140 (MQ=255)
                                                                                  gTTCGCCACAGAGCAACTGCTGATCTGGTCCGCCAGCGCCTTTATCACCAAAGCGCTGCTGGTACCGTTAATCATGACTTACGCTGCACGAAATATTCCCCAGAACATCCCGGAAAAAGCGTTATTCGGTCCGGCAatga                                                  <  1:309939/140‑1 (MQ=255)
                                                                                      gccgcAGAGCAACTGCTGATCTGGTCCGCCAGCGCCTTTATCACCAAAGCGCTGCTGGTACCGTTAATCATGACTTACGCTGCACGAAATATTCCCCAGAACATCCCGGAAAAAGCGTTATTCGGTCCGGCAATGATGGc                                              >  2:159011/1‑140 (MQ=255)
                                                                                      gccgcAGAGCAACTGCTGATCTGGTCCGCCAGCGCCTTTATCACCAAAGCGCTGCTGGTACCGTTAATCATGACTTACGCTGCACGAAATATTCCCCAGAACATCCCGGAAAAAGCGTTATTCGGTCCGGCAATGATGGc                                              <  2:591270/140‑1 (MQ=255)
                                                                                        cgcAGAGCAACTGCTGATCTGGTCCGCCAGCGCCTTTATCACCAAAGCGCTGCTGGTACCGTTAATCATGACTTACGCTGCACGAAATATTCCCCAGAACATCCCGGAAAAAGCGTTATTCGGTCCGGCAATGATGGCAc                                            >  1:60492/1‑140 (MQ=255)
                                                                                         gcAGAGCAACTGCTGATCTGGTCCGCCAGCGCCTTTATCACCAAAGCGCTGCTGGTACCGTTAATCATGACTTACGCTGCACGAAATATTCCCCAGAACATCCCGGAAAAAGCGTTATTCGGTCCGGCAATGATGGCACt                                           >  2:550928/1‑140 (MQ=255)
                                                                                               cAACTGCTGATCTGGTCCGCCAGCGCCTTTATCACCAAAGCGCTGCTGGTACCGTTAATCATGACTTACGCTGCACGAAATATTCCCCAGAACATCCCGGAAAAAGCGTTATTCGGTCCGGCAATGATGGCACTGCTcgc                                     <  1:344536/140‑1 (MQ=255)
                                                                                                       gATCTGGTCCGCCAGCGCCTTTATCACCAAAGCGCTGCTGGTACCGTTAATCATGACTTACGCTGCACGAAATATTCCCCAGAACATCCCGGAAAAAGCGTTATTCGGTCCGGCAATGATGGCACTGCTCGCGGCGTTaa                             >  1:116667/1‑140 (MQ=255)
                                                                                                               ccGCCAGCGCCTTTATCACCAAAGCGCTGCTGGTACCGTTAATCATGACTTACGCTGCACGAAATATTCCCCAGAACATCCCGGAAAAAGCGTTATTCGGTCCGGCAATGATGGCACTGCTCGCGGCGTTAATTGTCCTg                     <  1:384763/140‑1 (MQ=255)
                                                                                                                  ccAGCGCCTTTATCACCAAAGCGCTGCTGGTACCGTTAATCATGACTTACGCTGCACGAAATATTCCCCAGAACATCCCGGAAAAAGCGTTATTCGGTCCGGCAATGATGGCACTGCTCGCGGCGTTAATTGTCCTGCtt                  >  1:219957/1‑140 (MQ=255)
                                                                                                                       gcCTTTATCACCAAAGCGCTGCTGGTACCGTTAATCATGACTTACGCTGCACGAAATATTCCCCAGAACATCCCGGAAAAAGCGTTATTCGGTCCGGCAATGATGGCACTGCTCGCGGCGTTAATTGTCCTGCTTTgcgc             <  1:626149/140‑1 (MQ=255)
                                                                                                                                  cAAAGCGCTGCTGGTACCGTTAATCATGACTTACGCTGCACGAAATATTCCCCAGAACATCCCGGAAAAAGCGTTATTCGGTCCGGCAATGATGGCACTGCTCGCGGCGTTAATTGTCCTGCTTTGCGCATTTGTCGTTc  <  2:219957/140‑1 (MQ=255)
                                                                                                                                       |                                                                                                                                      
TCAAAAGCTATCGCCTGTCATGCGGATTTTACGCCTGCCAGTCACTGGTGCTGGTGTCTATTTTCGCCACTCTCTCGTGCCTGTTCGCCGCAGAGCAACTGCTGATCTGGTCCGCCAGCGCCTTTATCACCAAAGTGCTGCTGGTACCGTTAATCATGACTTACGCTGCACGAAATATTCCCCAGAACATCCCGGAAAAAGCGTTATTCGGTCCGGCAATGATGGCACTGCTCGCGGCGTTAATTGTCCTGCTTTGCGCATTTGTCGTTC  >  NC_000913/2606332‑2606601

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A