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 F1 I1 R1 1696 279.3 15874187 97.8% 15524954 93.0

Breseq alignment

N/A

GATK/CNVnator alignment

BRESEQ :: bam2aln output
GACCTATCACTGCAT‑AAATAATGTGATGCCGGGATGGTTT‑‑‑‑‑‑‑‑CCGCATC‑TTATAGCGAT‑‑CAGATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCGG  >  NC_000913/4474809‑4474949
                                                          |                                                                                              
GACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACC                                                            <  SRR4302543.851944/94‑1 (MQ=21)
GACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACC                                                            <  SRR4302543.3118758/94‑1 (MQ=21)
   CTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATC                                                         >  SRR4302543.1426244/1‑94 (MQ=16)
   CTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATC                                                         <  SRR4302543.2757877/94‑1 (MQ=16)
   CTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATC                                                         >  SRR4302543.7776263/1‑94 (MQ=16)
   CTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATC                                                         >  SRR4302543.3266033/1‑94 (MQ=16)
         CTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCT                                                   >  SRR4302543.4569656/1‑94 (MQ=16)
         CTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCT                                                   >  SRR4302543.7979933/1‑94 (MQ=16)
         CTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCT                                                   >  SRR4302543.3645443/1‑94 (MQ=16)
          TGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTT                                                  >  SRR4302543.3541283/1‑94 (MQ=18)
          TGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTT                                                  <  SRR4302543.4890165/94‑1 (MQ=18)
           GCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTT                                                 >  SRR4302543.6958130/1‑94 (MQ=19)
           GCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTT                                                 >  SRR4302543.4443342/1‑94 (MQ=19)
           GCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTT                                                 <  SRR4302543.5431335/94‑1 (MQ=19)
             ataAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGA                                               >  SRR4302543.972912/4‑94 (MQ=23)
              taAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGAT                                              <  SRR4302543.4620595/92‑1 (MQ=25)
              taAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGAT                                              >  SRR4302543.861384/3‑94 (MQ=25)
              A‑AAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATA                                             >  SRR4302543.602067/1‑94 (MQ=26)
              A‑AAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATA                                             >  SRR4302543.1439426/1‑94 (MQ=26)
                AAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAG                                            >  SRR4302543.7877603/1‑94 (MQ=28)
                AAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAG                                            <  SRR4302543.7533058/94‑1 (MQ=28)
                 AATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGT                                           >  SRR4302543.4774461/1‑94 (MQ=28)
                 AATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGT                                           <  SRR4302543.2810209/94‑1 (MQ=28)
                 AATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGT                                           >  SRR4302543.3001623/1‑94 (MQ=28)
                 AATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGT                                           >  SRR4302543.608000/1‑94 (MQ=28)
                  ATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTA                                          <  SRR4302543.5723611/94‑1 (MQ=28)
                  ATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTA                                          >  SRR4302543.5813870/1‑94 (MQ=28)
                   TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTAT                                         <  SRR4302543.4859727/94‑1 (MQ=28)
                   TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTAT                                         <  SRR4302543.4865326/94‑1 (MQ=28)
                   TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTAT                                         >  SRR4302543.942892/1‑94 (MQ=28)
                   TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTAT                                         <  SRR4302543.2744330/94‑1 (MQ=28)
                   TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGAACATCACCGCTTTGATAGTAT                                         >  SRR4302543.5144332/1‑94 (MQ=19)
                    AATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTATG                                        >  SRR4302543.1448068/1‑94 (MQ=30)
                    AATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTATG                                        <  SRR4302543.7581247/94‑1 (MQ=30)
                     ATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTATGC                                       <  SRR4302543.6102713/94‑1 (MQ=32)
                     ATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTATGC                                       >  SRR4302543.7213912/1‑94 (MQ=32)
                     ATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTATGC                                       <  SRR4302543.6102712/94‑1 (MQ=32)
                     ATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTATGC                                       >  SRR4302543.5815238/1‑94 (MQ=32)
                     ATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTATGC                                       >  SRR4302543.3265521/1‑94 (MQ=32)
                      TGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTATGCA                                      <  SRR4302543.2822586/94‑1 (MQ=34)
                      TGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTATGCA                                      >  SRR4302543.5460354/1‑94 (MQ=34)
                       GTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTATGCAT                                     <  SRR4302543.5592648/94‑1 (MQ=36)
                       GTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTATGCAT                                     >  SRR4302543.2551165/1‑94 (MQ=36)
                       GTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTATGCAT                                     <  SRR4302543.1837440/94‑1 (MQ=36)
                                                         TTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCG   <  SRR4302543.6704454/94‑1 (MQ=60)
                                                         TTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCG   <  SRR4302543.7180421/94‑1 (MQ=60)
                                                         TTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCG   >  SRR4302543.7235776/1‑94 (MQ=60)
                                                         TTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCG   <  SRR4302543.6048218/94‑1 (MQ=60)
                                                         TTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCG   <  SRR4302543.819050/94‑1 (MQ=60)
                                                          TATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCGG  <  SRR4302543.4107908/94‑1 (MQ=60)
                                                          |                                                                                              
GACCTATCACTGCAT‑AAATAATGTGATGCCGGGATGGTTT‑‑‑‑‑‑‑‑CCGCATC‑TTATAGCGAT‑‑CAGATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCGG  >  NC_000913/4474809‑4474949

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑