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 I2 R1 882 254.4 12957588 98.0% 12698436 93.0

Breseq alignment

N/A

GATK/CNVnator alignment

BRESEQ :: bam2aln output
GAATAGACCTATCACTGCAT‑AAATAATGTGATGCCGGGATGGTTT‑‑‑‑‑‑‑‑CCGCATC‑TTATAGCGAT‑‑CAGATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCGG  >  NC_000913/4474804‑4474949
                                                               |                                                                                              
GAATAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCG                                                                 >  SRR4302537.247759/1‑94 (MQ=30)
GAATAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCG                                                                 <  SRR4302537.4759440/94‑1 (MQ=30)
GAATAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCG                                                                 <  SRR4302537.2978680/94‑1 (MQ=30)
GAATAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCG                                                                 >  SRR4302537.621295/1‑94 (MQ=30)
  ATAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCG                                                               >  SRR4302537.4341550/1‑94 (MQ=26)
  ATAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCG                                                               >  SRR4302537.5540239/1‑94 (MQ=26)
  ATAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCG                                                               <  SRR4302537.4029834/94‑1 (MQ=26)
   TAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGA                                                              >  SRR4302537.1646246/1‑94 (MQ=25)
   TAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGA                                                              >  SRR4302537.5347447/1‑94 (MQ=25)
    AGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTCTTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGAC                                                             >  SRR4302537.2089035/1‑94 (MQ=23)
     GACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACC                                                            <  SRR4302537.3867132/94‑1 (MQ=23)
        CTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATC                                                         >  SRR4302537.487949/1‑94 (MQ=23)
          ATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCAC                                                       >  SRR4302537.4648192/1‑94 (MQ=23)
           TCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACC                                                      <  SRR4302537.3027262/94‑1 (MQ=23)
            CACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCG                                                     <  SRR4302537.3228022/94‑1 (MQ=23)
             ACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGC                                                    >  SRR4302537.930667/1‑94 (MQ=23)
              CTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCT                                                   >  SRR4302537.6356421/1‑94 (MQ=25)
              CTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCT                                                   <  SRR4302537.5318088/94‑1 (MQ=25)
                GCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTT                                                 <  SRR4302537.1713292/94‑1 (MQ=28)
                 CATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTG                                                <  SRR4302537.4623827/94‑1 (MQ=30)
                  ataAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGA                                               >  SRR4302537.6180365/4‑94 (MQ=33)
                  ataAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGA                                               <  SRR4302537.531612/91‑1 (MQ=33)
                   taAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGAT                                              <  SRR4302537.4668219/92‑1 (MQ=34)
                   A‑AAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATA                                             >  SRR4302537.1322193/1‑94 (MQ=36)
                   A‑AAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATA                                             >  SRR4302537.6468030/1‑94 (MQ=36)
                     AAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAG                                            >  SRR4302537.4567327/1‑94 (MQ=38)
                     AAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAG                                            <  SRR4302537.2645603/94‑1 (MQ=38)
                     AAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAG                                            <  SRR4302537.2590566/94‑1 (MQ=38)
                      AATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGT                                           <  SRR4302537.3885781/94‑1 (MQ=38)
                       ATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTA                                          >  SRR4302537.5475734/1‑94 (MQ=38)
                       ATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTA                                          >  SRR4302537.3692845/1‑94 (MQ=38)
                       ATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTA                                          >  SRR4302537.366057/1‑94 (MQ=38)
                       ATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTA                                          >  SRR4302537.2136905/1‑94 (MQ=38)
                        TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTAT                                         <  SRR4302537.1458606/94‑1 (MQ=38)
                        TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTAT                                         >  SRR4302537.524425/1‑94 (MQ=38)
                        TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTAT                                         <  SRR4302537.3192539/94‑1 (MQ=38)
                        TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTAT                                         <  SRR4302537.2864043/94‑1 (MQ=38)
                         AATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATG                                        <  SRR4302537.49300/94‑1 (MQ=40)
                         AATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATG                                        <  SRR4302537.563562/94‑1 (MQ=40)
                         AATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATG                                        <  SRR4302537.2891636/94‑1 (MQ=40)
                           TGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCA                                      <  SRR4302537.3543920/94‑1 (MQ=44)
                            GTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCAT                                     <  SRR4302537.4303624/94‑1 (MQ=46)
                            GTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCAT                                     <  SRR4302537.3897629/94‑1 (MQ=46)
                                                               TATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCGG  >  SRR4302537.4094050/1‑94 (MQ=60)
                                                               |                                                                                              
GAATAGACCTATCACTGCAT‑AAATAATGTGATGCCGGGATGGTTT‑‑‑‑‑‑‑‑CCGCATC‑TTATAGCGAT‑‑CAGATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCATACGGTTTTCCGCCTGATCAAAAACAATGCTGGCGG  >  NC_000913/4474804‑4474949

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑