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 1873 183.1 9376148 98.2% 9207377 93.0

Breseq alignment

N/A

GATK/CNVnator alignment

BRESEQ :: bam2aln output
CCACCGGAAAATTTACGTATAGCAATAGAACACTTTGGGTGGAAGAATAGACCTATCACTGCAT‑AAATAATGTGATGCCGGGATGGTTT‑‑‑‑‑‑‑‑CCGCATC‑TTATAGCGAT‑‑CAGATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCAT  >  NC_000913/4474760‑4474914
                                                                                         |                                                                             
CCACCGGAAAATTTACGTATAGCAATAGAACACTTTGGGTGGAAGAATAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTgtat                                                                           >  SRR4302535.900487/1‑90 (MQ=60)
CCACCGGAAAATTTACGTATAGCAATAGAACACTTTGGGTGGAAGAATAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTgtat                                                                           >  SRR4302535.4505126/1‑90 (MQ=60)
    CGGAAAATTTACGTATAGCAATAGAACACTTTGGGTGGAAGAATAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTgtatttcc                                                                       >  SRR4302535.1435924/1‑86 (MQ=60)
     GGAAAATTTACGTATAGCAATAGAACACTTTGGGTGGAAGAATAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTgtatttccc                                                                      >  SRR4302535.3506324/1‑85 (MQ=60)
             TACGTATAGCAATAGAACACTTTGGGTGGAAGAATAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTgtatttcccggcatctt                                                              >  SRR4302535.1375994/1‑77 (MQ=60)
              ACGTATAGCAATAGAACACTTTGGGTGGAAGAATAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTgtatttcccggcatcttt                                                             <  SRR4302535.2794405/94‑19 (MQ=60)
              ACGTATAGCAATAGAACACTTTGGGTGGAAGAATAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTgtatttcccggcatcttt                                                             <  SRR4302535.2235255/94‑19 (MQ=60)
                GTATAGCAATAGAACACTTTGGGTGGAAGAATAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTgtatttcccggcatctttat                                                           >  SRR4302535.3204602/1‑74 (MQ=60)
                GTATAGCAATAGAACACTTTGGGTGGAAGAATAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTgtatttcccggcatctttat                                                           >  SRR4302535.2287071/1‑74 (MQ=60)
                  ATAGCAATAGAACACTTTGGGTGGAAGAATAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTgtatttcccggcatctttatag                                                         >  SRR4302535.2757351/1‑72 (MQ=60)
                   TAGCAATAGAACACTTTGGGTGGAAGAATAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTgtatttcccggcatctttatagc                                                        >  SRR4302535.1688411/1‑71 (MQ=60)
                    AGCAATAGAACACTTTGGGTGGAAGAATAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTgtatttcccggcatctttatagcg                                                       >  SRR4302535.1142986/1‑70 (MQ=60)
                      GAATAGAACACTTTGGGTGGAAGAATAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTgtatttcccggcatctttatagcgat                                                     <  SRR4302535.2270553/94‑27 (MQ=60)
                       AATAGAACACTTTGGGTGGAAGAATAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTgtatttcccggcatctttatagcgata                                                    >  SRR4302535.953092/1‑67 (MQ=60)
                          AGAACACTTTGGGTGGAAGAATAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTgtatttcccggcatctttatagcgatagca                                                 >  SRR4302535.649343/1‑64 (MQ=60)
                          AGAACACTTTGGGTGGAAGAATAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTgtatttcccggcatctttatagcgatagca                                                 >  SRR4302535.302242/1‑64 (MQ=60)
                          AGAACACTTTGGGTGGAAGAATAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTgtatttcccggcatctttatagcgatagca                                                 >  SRR4302535.181666/1‑64 (MQ=60)
                          AGAACACTTTGGGTGGAAGAATAGACCTATCACTGCATAAAATAATGCGATGCCGGGATGGTTTgtatttcccggcatctttatagcgatagca                                                 >  SRR4302535.4361214/1‑64 (MQ=60)
                            AACACTTTGGGTGGAAGAATAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTgtatttcccggcatctttatagcgatagcact                                               >  SRR4302535.4358003/1‑62 (MQ=60)
                              CACTTTGGGTGGAAGAATAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTgtatttcccggcatctttatagcgatagcaatta                                             >  SRR4302535.4257517/1‑60 (MQ=60)
                                CTTTGGGTGGAAGAATAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTgtatttcccggcatctttatagcgatagcaattatt                                           >  SRR4302535.4084121/1‑58 (MQ=60)
                                CTTTGGGTGGAAGAATAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTggatttcccggcatctttatagcgatagcaattatt                                           >  SRR4302535.1823135/1‑58 (MQ=60)
                                   TGGGTGGAAGAATAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTgtatttcccggcatctttatagcgatagcaattatttac                                        <  SRR4302535.2468658/94‑40 (MQ=60)
                                     GGTGGAAGAATAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTgtatttcccggcatctttatagcgatagcaattatttactg                                      <  SRR4302535.2936663/94‑42 (MQ=60)
                                       TGGAAGAATAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTgtatttcccggcatctttatagcgatagcaattatttactgag                                    >  SRR4302535.4411170/1‑51 (MQ=60)
                                        GGAAGAATAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTgtatttcccggcatctttatagcgatagcaattatttactgagt                                   >  SRR4302535.109954/1‑50 (MQ=60)
                                         GAAGAATAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTgtatttcccggcatctttatagcgatagcaattatttactgagtg                                  <  SRR4302535.2235951/94‑46 (MQ=60)
                                          AAGAATAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTgtatttcccggcatctttatagcgatagcaattatttactgagtgt                                 >  SRR4302535.1747824/1‑48 (MQ=60)
                                          AAGAATAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTgtatttcccggcatctttatagcgatagcaattatttactgagtgt                                 >  SRR4302535.1822293/1‑48 (MQ=60)
                                             AATAGACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTgtatttcccggcatctttatagcgatagcaattatttactgagtgtcgc                              >  SRR4302535.2958452/1‑45 (MQ=60)
                                                   CCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCAT                       >  SRR4302535.4673479/1‑94 (MQ=18)
                                                    CTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATC                      >  SRR4302535.256948/1‑94 (MQ=16)
                                                    CTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATC                      >  SRR4302535.608446/1‑94 (MQ=16)
                                                          CTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCT                <  SRR4302535.1583109/94‑1 (MQ=16)
                                                          CTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCT                >  SRR4302535.3109987/1‑94 (MQ=16)
                                                             CATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTG             <  SRR4302535.3310029/94‑1 (MQ=21)
                                                               taAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGAT           <  SRR4302535.2479488/92‑1 (MQ=25)
                                                               A‑AAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATA          >  SRR4302535.1351298/1‑94 (MQ=26)
                                                                 AAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAG         >  SRR4302535.1228544/1‑94 (MQ=28)
                                                                  AATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGT        >  SRR4302535.51271/1‑94 (MQ=28)
                                                                   ATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTA       <  SRR4302535.358320/94‑1 (MQ=28)
                                                                    TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTAT      >  SRR4302535.2127482/1‑94 (MQ=28)
                                                                     AATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTATG     >  SRR4302535.3517061/1‑94 (MQ=30)
                                                                      ATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTATGC    <  SRR4302535.2319897/94‑1 (MQ=32)
                                                                      ATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTATGC    >  SRR4302535.2379915/1‑94 (MQ=32)
                                                                      ATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTCGATAGTATGC    >  SRR4302535.4602569/1‑94 (MQ=23)
                                                                        GTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTATGCAT  <  SRR4302535.4394344/94‑1 (MQ=36)
                                                                                         |                                                                             
CCACCGGAAAATTTACGTATAGCAATAGAACACTTTGGGTGGAAGAATAGACCTATCACTGCAT‑AAATAATGTGATGCCGGGATGGTTT‑‑‑‑‑‑‑‑CCGCATC‑TTATAGCGAT‑‑CAGATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCAT  >  NC_000913/4474760‑4474914

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 2 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑