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 1548 369.5 20095359 96.9% 19472402 93.0

Breseq alignment

N/A

GATK/CNVnator alignment

BRESEQ :: bam2aln output
GACCTATCACTGCAT‑AAATAATGTGATGCCGGGATGGTTT‑‑‑‑‑‑‑‑CCGCATC‑TTATAGCGAT‑‑CAGATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCAT  >  NC_000913/4474809‑4474914
                                                  |                                                                   
GACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACC                         <  SRR4302540.5321681/94‑1 (MQ=21)
GACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACC                         >  SRR4302540.4991003/1‑94 (MQ=21)
 ACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCA                        <  SRR4302540.4338892/94‑1 (MQ=19)
 ACCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCA                        <  SRR4302540.3740554/94‑1 (MQ=19)
  CCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCAT                       >  SRR4302540.506075/1‑94 (MQ=18)
  CCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCAT                       >  SRR4302540.2168524/1‑94 (MQ=18)
  CCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCAT                       >  SRR4302540.9161752/1‑94 (MQ=18)
  CCTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCAT                       >  SRR4302540.2953111/1‑94 (MQ=18)
   CTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATC                      >  SRR4302540.3718382/1‑94 (MQ=16)
   CTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATC                      <  SRR4302540.592258/94‑1 (MQ=16)
   CTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATC                      >  SRR4302540.798401/1‑94 (MQ=16)
   CTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATC                      <  SRR4302540.8161739/94‑1 (MQ=16)
   CTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATC                      >  SRR4302540.8324768/1‑94 (MQ=16)
   CTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATC                      >  SRR4302540.8493199/1‑94 (MQ=16)
   CTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATC                      >  SRR4302540.148963/1‑94 (MQ=16)
   CTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATC                      >  SRR4302540.8591999/1‑94 (MQ=16)
   CTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATC                      >  SRR4302540.1476522/1‑94 (MQ=16)
   CTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATC                      <  SRR4302540.9714736/94‑1 (MQ=16)
   CTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATC                      >  SRR4302540.2028219/1‑94 (MQ=16)
   CTATCACTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGCGTCGCGACCATC                      >  SRR4302540.2048714/1‑94 (MQ=23)
         CTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCT                >  SRR4302540.1926329/1‑94 (MQ=16)
         CTGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCT                >  SRR4302540.4032074/1‑94 (MQ=16)
          TGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTT               >  SRR4302540.4263756/1‑94 (MQ=18)
          TGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTT               >  SRR4302540.8028560/1‑94 (MQ=18)
          TGCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTT               <  SRR4302540.5324403/94‑1 (MQ=18)
           GCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTT              <  SRR4302540.8457007/94‑1 (MQ=19)
           GCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTT              <  SRR4302540.5305191/94‑1 (MQ=19)
           GCATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTT              <  SRR4302540.5082988/94‑1 (MQ=19)
            CATAAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTG             <  SRR4302540.4478167/94‑1 (MQ=21)
              taAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGAT           <  SRR4302540.4414101/92‑1 (MQ=25)
              taAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGAT           >  SRR4302540.7621205/3‑94 (MQ=25)
              taAAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGAT           >  SRR4302540.4784050/3‑94 (MQ=25)
              A‑AAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATA          <  SRR4302540.2520939/94‑1 (MQ=26)
                AAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAG         <  SRR4302540.9942271/94‑1 (MQ=28)
                AAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAG         <  SRR4302540.8148785/94‑1 (MQ=28)
                AAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAG         <  SRR4302540.1329157/94‑1 (MQ=28)
                AAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAG         <  SRR4302540.5675654/94‑1 (MQ=28)
                AAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAG         <  SRR4302540.1329158/94‑1 (MQ=28)
                AAATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAG         <  SRR4302540.5278586/94‑1 (MQ=28)
                 AATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGT        >  SRR4302540.7317161/1‑94 (MQ=28)
                 AATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGT        <  SRR4302540.7159051/94‑1 (MQ=28)
                 AATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGT        <  SRR4302540.4807048/94‑1 (MQ=28)
                 AATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGT        <  SRR4302540.8123676/94‑1 (MQ=28)
                 AATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGT        <  SRR4302540.3314596/94‑1 (MQ=28)
                 AATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGT        >  SRR4302540.3055062/1‑94 (MQ=28)
                  ATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTA       <  SRR4302540.8363711/94‑1 (MQ=28)
                  ATAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTA       <  SRR4302540.2228840/94‑1 (MQ=28)
                   TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTAT      <  SRR4302540.9798773/94‑1 (MQ=28)
                   TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTAT      <  SRR4302540.1675118/94‑1 (MQ=28)
                   TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTAT      <  SRR4302540.3990867/94‑1 (MQ=28)
                   TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTAT      <  SRR4302540.9457166/94‑1 (MQ=28)
                   TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTAT      <  SRR4302540.2223320/94‑1 (MQ=28)
                   TAATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTAT      <  SRR4302540.2521728/94‑1 (MQ=28)
                    AATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTATG     <  SRR4302540.7427419/94‑1 (MQ=30)
                    AATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTATG     <  SRR4302540.8757622/94‑1 (MQ=30)
                     ATGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTATGC    >  SRR4302540.2642234/1‑94 (MQ=32)
                      TGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTATGCA   >  SRR4302540.809638/1‑94 (MQ=34)
                      TGTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTATGCA   >  SRR4302540.9458874/1‑94 (MQ=34)
                       GTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTATGCAT  <  SRR4302540.8851011/94‑1 (MQ=36)
                       GTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTATGCAT  <  SRR4302540.3221372/94‑1 (MQ=36)
                       GTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTATGCAT  <  SRR4302540.9668553/94‑1 (MQ=36)
                       GTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTATGCAT  <  SRR4302540.7624093/94‑1 (MQ=36)
                       GTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTATGCAT  <  SRR4302540.7451351/94‑1 (MQ=36)
                       GTGATGCCGGGATGGTTTGTATTTCCCGGCATCTTTATAGCGATAGCA‑ATTATTTACTGAGTGTCGCGACCATCACCGCTTTGATAGTATGCAT  <  SRR4302540.5769552/94‑1 (MQ=36)
                                                  |                                                                   
GACCTATCACTGCAT‑AAATAATGTGATGCCGGGATGGTTT‑‑‑‑‑‑‑‑CCGCATC‑TTATAGCGAT‑‑CAGATTATTTACTGAGCGTCGCGACCATCACCGCTTTGATAGTATGCAT  >  NC_000913/4474809‑4474914

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑