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 26 102.0 3326124 78.0% 2594376 98.8

Breseq alignment

N/A

GATK/CNVnator alignment

BRESEQ :: bam2aln output
GGGCCCAAAACCAACAATTTGGGTGGCCCATTTCCTAC‑TTTTCAATGAACCCAAAACCAACATTTTTAGATGGCCCTTGACACTCTACTCTAAATCTAATGAAAGCTCCGTCTCTAAAGCTGATTTTCTAGAATTAAAAAGACAACT  >  CP002094/675632‑675778
                                                 |                                                                                                  
GGGCCCAAAACCAACAATTTGGGTGGCCCATTTCCTACATTTTCAATG‑ACCCAAAACCAACATTTTTAGATGGCCCTTGACACTCTACTCTAAATCTAAT                                                 >  SRR7892090.738706/1‑100 (MQ=0)
 GGCCCAAAACCAACAATTTGGGTGGCCCATTTCCTACATTTTCAATG‑ACCCAAAACCAACATTTTTAGATGGCCCTTGACACTCTACTCTAAATCTAATG                                                >  SRR7892090.988501/1‑100 (MQ=0)
 GGCCCAAAACCAACAATTTGGGTGGCCCATTTCCTACATTTTCAATG‑ACCCAAAACCAACATTTTTAGATGGCCCTTGACACTCTACTCTAAATCTAATG                                                <  SRR7892090.742789/100‑1 (MQ=0)
    CCAAAACCAACAATTTGGGTGGCCCATTTCCTACATTTTCAATG‑ACCCAAAACCAACATTTTTAGATGGCCCTTGACACTCTACTCTAAATCTAATGAAA                                             >  SRR7892090.523825/1‑100 (MQ=1)
      AAAACCAACAATTTGGGTGGCCCATTTCCTACATTTTCAATG‑ACCCAAAACCAACATTTTTAGATGGCCCTTGACACTCTACTCTAAATCTAATGAAAGC                                           <  SRR7892090.1120376/100‑1 (MQ=11)
       AAACCAACAATTTGGGTGGCCCATTTCCTACATTTTCAATG‑ACCCAAAACCAACATTTTTAGATGGCCCTTGACACTCTACTCTAAATCTAATGAAAGCT                                          <  SRR7892090.841595/100‑1 (MQ=13)
       AAACCAACAATTTGGGTGGCCCATTTCCTACATTTTCAATG‑ACCCAAAACCAACATTTTTAGATGGCCCTTGACACTCTACTCTAAATCTAATGAAAGCT                                          <  SRR7892090.1491063/100‑1 (MQ=13)
        AACCAACAATTTGGGTGGCCCATTTCCTACATTTTCAATG‑ACCCAAAACCAACATTTTTAGATGGCCCTTGACACTCTACTCTAAATCTAATGAAAGCTC                                         <  SRR7892090.358887/100‑1 (MQ=18)
         ACCAACAATTTGGGTGGCCCATTTCCTACATTTTCAATG‑ACCCAAAACCAACATTTTTAGATGGCCCTTGACACTCTACTCTAAATCTAATGAAAGCTCC                                        <  SRR7892090.1154414/100‑1 (MQ=20)
             ACAATTTGGGTGGCCCATTTCCTACATTTTCAATG‑ACCCAAAACCAACATTTTTAGATGGCCCTTGACACTCTACTCTAAATCTAATGAAAGCTCCGTCT                                    <  SRR7892090.759551/100‑1 (MQ=29)
                ATTTGGGTGGCCCATTTCCTACATTTTCAATG‑ACCCAAAACCAACATTTTTAGATGGCCCTTGACACTCTACTCTAAATCTAATGAAAGCTCCGTCTCTA                                 >  SRR7892090.1114596/1‑100 (MQ=36)
                   TGGGTGGCCCATTTCCTACATTTTCAATG‑ACCCAAAACCAACATTTTTAGATGGCCCTTGACACTCTACTCTAAATCTAATGAAAGCTCCGTCTCTAAAG                              <  SRR7892090.1404501/100‑1 (MQ=43)
                   TGGGTGGCCCATTTCCTACATTTTCAATG‑ACCCAAAACCAACATTTTTAGATGGCCCTTGACACTCTACTCTAAATCTAATGAAAGCTCCGTCTCTAAAG                              <  SRR7892090.1130498/100‑1 (MQ=43)
                         GCCCATTTCCTACATTTTCAATG‑ACCCAAAACCAACATTTTTAGATGGCCCTTGACACTCTACTCTAAATCTAATGAAAGCTCCGTCTCTAAAGCTGATT                        >  SRR7892090.174804/1‑100 (MQ=57)
                           CCATTTCCTACATTTTCAATG‑ACCCAAAACCAACATTTTTAGATGGCCCTTGACACTCTACTCTAAATCTAATGAAAGCTCCGTCTCTAAAGCTGATTTT                      >  SRR7892090.1572088/1‑100 (MQ=60)
                            CATTTCCTACATTTTCAATG‑ACCCAAAACCAACATTTTTAGATGGCCCTTGACACTCTACTCTAAATCTAATGAAAGCTCCGTCTCTAAAGCTGATTTTC                     <  SRR7892090.113509/100‑1 (MQ=60)
                             ATTTCCTACATTTTCAATG‑ACCCAAAACCAACATTTTTAGATGGCCCTTGACACTCTACTCTAAATCTAATGAAAGCTCCGTCTCTAAAGCTGATTTTCT                    >  SRR7892090.1520516/1‑100 (MQ=60)
                              TTTCCTACATTTTCAATG‑ACCCAAAACCAACATTTTTAGATGGCCCTTGACACTCTACTCTAAATCTAATGAAAGCTCCGTCTCTAAAGCTGATTTTCTA                   >  SRR7892090.1383570/1‑100 (MQ=60)
                                TCCTACATTTTCAATG‑ACCCAAAACCAACATTTTTAGATGGCCCTTGACACTCTACTCTAAATCTAATGAAAGCTCCGTCTCTAAAGCTGATTTTCTAGA                 <  SRR7892090.400008/100‑1 (MQ=60)
                                 CCTACATTTTCAATG‑ACCCAAAACCAACATTTTTAGATGGCCCTTGACACTCTACTCTAAATCTAATGAAAGCTCCGTCTCTAAAGCTGATTTTCTAGAA                >  SRR7892090.1050192/1‑100 (MQ=60)
                                  CTACATTTTCAATG‑ACCCAAAACCAACATTTTTAGATGGCCCTTGACACTCTACTCTAAATCTAATGAAAGCTCCGTCTCTAAAGCTGATTTTCTAGAAT               <  SRR7892090.1593055/100‑1 (MQ=60)
                                  CTACATTTTCAATG‑ACCCAAAACCAACATTTTTAGATGGCCCTTGACACTCTACTCTAAATCTAATGAAAGCTCCGTCTCTAAAGCTGATTTTCTAGAAT               >  SRR7892090.986595/1‑100 (MQ=60)
                                    acaTTTTCAATG‑ACCCAAAACCAACATTTTTAGATGGCCCTTGACACTCTACTCTAAATCTAATGAAAGCTCCGTCTCTAAAGCTGATTTTCTAGAATTA             >  SRR7892090.288311/4‑100 (MQ=60)
                                     caTTTTCAATG‑ACCCAAAACCAACATTTTTAGATGGCCCTTGACACTCTACTCTAAATCTAATGAAAGCTCCGTCTCTAAAGCTGATTTTCTAGAATTAA            >  SRR7892090.632532/3‑100 (MQ=60)
                                          TCAATG‑ACCCAAAACCAACATTTTTAGATGGCCCTTGACACTCTACTCTAAATCTAATGAAAGCTCCGTCTCTAAAGCTGATTTTCTAGAATTAAAAAGA       <  SRR7892090.634643/100‑1 (MQ=60)
                                           CAATG‑ACCCAAAACCAACATTTTTAGATGGCCCTTGACACTCTACTCTAAATCTAATGAAAGCTCCGTCTCTAAAGCTGATTTTCTAGAATTAAAAAGAC      <  SRR7892090.1656553/100‑1 (MQ=60)
                                                GACCCAAAACCAACATTTTTAGATGGCCCTTGACACTCTACTCTAAATCTAATGAAAGATCCGTCTCTAAAGCTGATTTTCTAGAATTAAAAAGACAACT  >  SRR7892090.1663744/1‑100 (MQ=60)
                                                 |                                                                                                  
GGGCCCAAAACCAACAATTTGGGTGGCCCATTTCCTAC‑TTTTCAATGAACCCAAAACCAACATTTTTAGATGGCCCTTGACACTCTACTCTAAATCTAATGAAAGCTCCGTCTCTAAAGCTGATTTTCTAGAATTAAAAAGACAACT  >  CP002094/675632‑675778

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑