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
A37 F60 I1 R1 14 60.0 2022092 98.7% 1995804 139.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,815,883 +C coding (667/687 nt) rph ← truncated RNase PH

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,815,8791.C87.2% 126.0 / 11.2 39coding (671/687 nt)rphtruncated RNase PH
Reads supporting (aligned to +/- strand):  ref base . (2/3);  new base C (14/20);  total (16/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑T‑C‑C‑CC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTC  >  NC_000913/3815746‑3816012
                                                                                                                                       |                                                                                                                                        
aaCTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑T‑c‑c‑ccct                                                                                                                                  <  1:722349/140‑3 (MQ=255)
    ggCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑C‑CC‑TCggg                                                                                                                              <  1:179378/140‑1 (MQ=255)
     gcgcTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑C‑CC‑TCGGGc                                                                                                                             <  2:96641/140‑1 (MQ=255)
      cgcTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCTAGCGCCGCGTTCAGCGTCGCTACAATGGATCCGAT‑TCC‑C‑CC‑TCGGGcc                                                                                                                            >  2:306299/1‑140 (MQ=255)
          gATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACGGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCACCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑C‑CC‑TCGGGCCagag                                                                                                                        <  1:654399/140‑1 (MQ=255)
          gATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑C‑CC‑TCGGGCCagag                                                                                                                        <  1:42730/140‑1 (MQ=255)
          gATATGGTTTCATGCCTCCGCTCCTCATCTTCCTTTTCTTCAGACAAACAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑C‑CC‑TCGGGCCagag                                                                                                                        <  2:287799/140‑1 (MQ=255)
               ggTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑C‑CC‑TCGGGCCAGAGCcaac                                                                                                                   <  1:818205/140‑1 (MQ=255)
                     aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGGGTCGCTACGATGGATTGGAT‑T‑C‑C‑CCGTCGGACCAGAGCCAACAAGATg                                                                                                             >  2:263114/1‑140 (MQ=255)
                     aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑C‑CC‑TCGGGCCAGAGCCAACAAGATg                                                                                                             >  1:852314/1‑140 (MQ=255)
                     aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAAGGGATTCGTT‑T‑CAC‑CG‑TCGGGCCAGAGCCAACAAGATg                                                                                                             >  1:364836/1‑140 (MQ=255)
                       gCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑C‑CC‑TCGGGCCAGAGCCAACAAGATGAg                                                                                                           <  2:714391/140‑1 (MQ=255)
                          ttCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCATTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑C‑CC‑TCGGGCCAGAGCCAACAAGATGAGTAg                                                                                                        <  2:204747/140‑1 (MQ=255)
                           tCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑C‑CC‑TCGGGCCAGAGCCAACAAGATGAGTAGc                                                                                                       >  1:852127/1‑140 (MQ=255)
                           tCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGCGGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTACGTCGCAACAATGGAGTCGGT‑T‑CGC‑CC‑TCGGGGCAGAGCCAACAAGATGAGTAGc                                                                                                       >  2:276877/1‑140 (MQ=255)
                               tcctcATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCACCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑C‑CC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCtt                                                                                                   <  1:19293/140‑1 (MQ=255)
                                         aCTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑C‑CC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGaa                                                                                         >  2:919922/1‑140 (MQ=255)
                                         aCTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑C‑CC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGaa                                                                                         <  1:877832/140‑1 (MQ=255)
                                                    gACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑C‑CC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCtt                                                                              <  1:574520/140‑1 (MQ=255)
                                                       aaaaaaaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑C‑CC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTg                                                                           >  1:307/1‑140 (MQ=255)
                                                         aaaaaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑C‑CC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGcc                                                                         >  1:179781/1‑140 (MQ=255)
                                                            aaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑C‑CC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTc                                                                      <  1:542090/140‑1 (MQ=255)
                                                                 cGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑C‑CC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                                                 <  2:707650/140‑1 (MQ=255)
                                                                   aCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑C‑CC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCa                                                               >  2:715491/1‑140 (MQ=255)
                                                                      catcaGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑C‑CC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACtt                                                            <  1:497847/140‑1 (MQ=255)
                                                                             cGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑C‑CC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAatgat                                                     >  2:728322/1‑140 (MQ=255)
                                                                                 ttAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑C‑CC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATgcgc                                                 <  1:881042/140‑1 (MQ=255)
                                                                                 ttAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑C‑CC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCGCGCATTCTGCCGTCCCCCGCACTTCAATGATgcgc                                                 >  2:342299/1‑140 (MQ=255)
                                                                                        tCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑C‑CC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCtt                                          <  2:829008/140‑1 (MQ=255)
                                                                                            tttGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑C‑CC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGt                                      <  2:585538/140‑1 (MQ=255)
                                                                                               gCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑C‑CC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGtcat                                   <  1:715491/140‑1 (MQ=255)
                                                                                                    cgccgcCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑C‑CC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTa                              >  1:502857/1‑140 (MQ=255)
                                                                                                    cgccgcCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑C‑CC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTAAATGATGCGCCCGTCTTCGGTCATCACTa                              >  1:323661/1‑140 (MQ=255)
                                                                                                    cgccgcCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑C‑CC‑TCGGGCCAGAGCCAACAAGATGAATAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTa                              >  2:584225/1‑140 (MQ=255)
                                                                                                      ccgccTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑C‑CC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACg                            >  2:654678/1‑140 (MQ=255)
                                                                                                                 gTCGCTACAATGGATTCTAT‑T‑CTC‑CC‑TCGGGGCAGAGCCAACAAGATGTGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGt                 <  2:364836/140‑1 (MQ=255)
                                                                                                                   cGCTACAATGGATTCGAT‑TCC‑C‑CC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGtct               >  2:734105/1‑140 (MQ=255)
                                                                                                                      tACAATGGATTCGATCC‑C‑C‑CC‑TCGGACCACAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTg            <  1:342299/140‑1 (MQ=255)
                                                                                                                         aaTGGATTCGAT‑TCC‑C‑CC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTTAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCgg         <  2:824602/140‑1 (MQ=255)
                                                                                                                         aaTGGATTCGAT‑T‑C‑CACC‑TCGGACCCGAGACAACAAGCTGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCgg         <  1:263114/140‑1 (MQ=255)
                                                                                                                           tGGATTCGAT‑TCC‑C‑CC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCa       <  2:852314/140‑1 (MQ=255)
                                                                                                                             gattcgat‑tcC‑C‑CC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCaga     <  2:852127/140‑1 (MQ=255)
                                                                                                                               ttcgat‑tcC‑C‑CC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGCCATCACTACGTTAATGTTGGTCTCTGCGGCAGAGt   >  2:367475/1‑140 (MQ=255)
                                                                                                                                tcgat‑tcC‑C‑CC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTc  >  2:565133/1‑140 (MQ=255)
                                                                                                                                tcgat‑tcC‑C‑CC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACGACGATCGTGTCGGGCTCTGCGGCAGAGTc  >  1:281280/1‑140 (MQ=255)
                                                                                                                                       |                                                                                                                                        
AACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑T‑C‑C‑CC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTC  >  NC_000913/3815746‑3816012

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A