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 150 26.0 2053212 90.0% 1847890 107.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA AM260479 582,589 T→G H295Q (CAT→CAG)  h16_A0555 → zinc metalloprotease

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*AM260479582,5890TG100.0% 36.8 / NA 11H295Q (CAT→CAG) h16_A0555zinc metalloprotease
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base G (6/5);  total (6/5)

GGCAGGGCGCGGCCATCGCCAACCAGCTGTCGTTCTCGCGCGGGGCCGAGCGCGAGGCCGACCGGGTCGGCTTCCAGATCCTGACCGCGGCGGGGTTTGACCCGCATGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATCGGGGACCGCGGAAAATTCGGTCCCGTCTTATGTGCGGACTCACCCGCTGACCTCCGAGCGGATTGCCGACATGCAGGACCGCG  >  AM260479/582483‑582710
                                                                                                          |                                                                                                                         
ggcAGGGCGCGGCCATCGCCAACCAGCTGTCGTTCTCGCGCGGGGCCGAGCGCGAGGCCGACCGGGTCGGCTTCCAGATCCTGACCGCGGCGGGGTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCGGCTg                                                                                                <  2:596272/134‑1 (MQ=255)
    gggCGCGGCCATCGCCAACCAGCTGTCGTTCTCGCGCGGGGCCGAGCGCGAGGCCGACCGGGTCGGCTTCCAGATCCTGACCGCGGCGGGGTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCGGCTGCAgc                                                                                            >  2:981899/1‑134 (MQ=255)
                    aaCCAGCTGTCGTTCTCGCGCGGGGCCGAGCGCGAGGCCGACCGGGTCGGCTTCCAGATCCTGACCGCGGCGGGGTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATCGGGGACcgc                                                                            >  2:300481/1‑134 (MQ=255)
                             tCGTTCTCGCGCGGGGCCGAGCGCGAGGCCGACCGGGTCGGCTTCCAGATCCTGACCGCGGCGGGGTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATCGGGGACCGCGGAAAAtt                                                                    <  1:300481/133‑1 (MQ=255)
                                                           gACCGGGTCGGCTTCCAGATCCTGACCGCGGCGGGGTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATCGGGGACCGCGGAAAATTCGGTCCCGTCTTATGTGCGGACTCACCCGCt                                     >  2:178712/1‑134 (MQ=255)
                                                                          cAGATCCTGACCGCGGCGGGGTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCGGCTGCa                                                                                              <  1:761213/62‑1 (MQ=255)
                                                                          cAGATCCTGACCGCGGCGGGGTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCGGCTGCa                                                                                              >  2:761213/1‑62 (MQ=255)
                                                                                       cggcggGGTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATCGGGGACCGCGGAAAATTc                                                                   <  1:55973/76‑1 (MQ=255)
                                                                                       cggcggGGTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATCGGGGACCGCGGAAAATTc                                                                   >  2:55973/1‑76 (MQ=255)
                                                                                       cggcggGGTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATCGGGGACCGCGGAAAATTCGGTCCCGTCTTATGTGCGGACTCACCCGCTGACCTCCGAGCGGATTGCCGACATGCAg         >  1:842950/1‑134 (MQ=255)
                                                                                              gTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATCGGGGACCGCGGAAAATTCGGTCCCGTCTTATGTGCGGACTCACCCGCTGACCTCCGAGCGGATTGCCGACATGCAGGACcgcg  <  1:1026307/134‑1 (MQ=255)
                                                                                                          |                                                                                                                         
GGCAGGGCGCGGCCATCGCCAACCAGCTGTCGTTCTCGCGCGGGGCCGAGCGCGAGGCCGACCGGGTCGGCTTCCAGATCCTGACCGCGGCGGGGTTTGACCCGCATGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATCGGGGACCGCGGAAAATTCGGTCCCGTCTTATGTGCGGACTCACCCGCTGACCTCCGAGCGGATTGCCGACATGCAGGACCGCG  >  AM260479/582483‑582710

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

BRESEQ :: bam2aln output
GACGCCGCGGCGGCGCTGGCCATGGGCGGGCAGGGCGCGGCCATCGCCAACCAGCTGTCGTTCTCGCGCGGGGCCGAGCGCGAGGCCGACCGGGTCGGCTTCCAGATCCTGACCGCGGCGGGGTTTGACCCGCATGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATCGGGGACCGCGGAAAATTCGGTCCCGTCTTATGTGCGGACTCACCCGCTGACCTCCGAGCGGATTGCCGACATGCAGGACCGCGTCAGCCATGCCAGCAAGCGCAAGGT  >  AM260479/582455‑582735
                                                                                                                                      |                                                                                                                                                  
GACGCCGCGGCGGCGCTGGCCATGGGCGGGCAGGGCGCGGCCATCGCCAACCAGCTGTCGTTCTCGCGCGGGGCCGAGCGCGAGGCCGACCGGGTCGGCTTCCAGATCCTGACCGCGGCGGGGTTTGACCCGCAGGGCATGCCCGATTTC                                                                                                                                     <  GWNJ‑0478:712:GW2002102894th:2:1206:12733:26776/150‑1 (MQ=60)
                             aagacggcatacgagatgtagctccgtctcgtgggctcgagatgtgtataagagacagGACCGGGTCGGCTTCCAGATCCTGACCGCGGCGGGGTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATCGGGGAC                                                                                                        <  GWNJ‑0478:712:GW2002102894th:2:2116:4260:67709/92‑1 (MQ=60)
                                                        atgtagctccgtctcgtgggctcggagatgtgtataagagacagTCCAGATCCTGACCGCGGCGGGGTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATCGGGGACCGCGGAAAATTCGGTCCCGTCTTATGT                                                                             <  GWNJ‑0478:712:GW2002102894th:2:1102:9870:83040/106‑1 (MQ=60)
                                                        GTCGTTCTCGCGCGGGGCCGAGCGCGAGGCCGACCGGGTCGGCTTCCAGATCCTGACCGCGGCGGGGTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATCGGGGACCGCGGAAAATTCGGTCCCGTCTTATG                                                                              <  GWNJ‑0478:712:GW2002102894th:2:1205:20490:30235/149‑1 (MQ=60)
                                                                                                GGCTTCCAGATCCTGACCGCGGCGGGGTTTGACCCGCAGGGCATGCCCtgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttctgcttgaaaaaaaaaaaaaaaaagaatgccaaagacagcaa                                       >  GWNJ‑0478:712:GW2002102894th:2:1215:20668:26939/1‑48 (MQ=60)
                                                                                                    TCCAGATCCTGACCGCGGCGGGGTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATCGGGGACCGCGGAAAATTCGGTCCCGTCTTATGTGCGGACTCACCCGCTGACCTCCGAGCGGATTGCCGACATGCAGG                                 >  GWNJ‑0478:712:GW2002102894th:2:2209:9535:13019/1‑150 (MQ=60)
                                                                                                                         GGTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATCGGGGACCGCGGAAAATTCGGTCCCGTCTTATGTGCGGACTCACCCGCTGACCTCCGAGCGGATTGCCGACATGCAGGACCGCGTCAGCCATGCCAGCA            <  GWNJ‑0478:712:GW2002102894th:2:2216:2858:99320/150‑1 (MQ=60)
                                                                                                                          GTTTGACCCGCAGGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATCGGGGACCGCGGAAAATTCGGTCCCGTCTTATGTGCGGACTCACCCGCTGACCTCCGAGCGGATTGCCGACATGCAGGACCGCGTCAGCCATGCCAGCA            >  GWNJ‑0478:712:GW2002102894th:2:2215:1857:12613/1‑149 (MQ=60)
                                                                                                                                CCCGCAGGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATCGGGGACCGCGGAAAATTCGGTCCCGTCTTATGTGCGGACTCACCCGCTGACCTCCGAGCccacgagacggagctacatctcgtatgccgtcttctgcttgaaaa      >  GWNJ‑0478:712:GW2002102894th:2:2201:5073:65620/1‑104 (MQ=60)
                                                                                                                                   GCAGGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATCGGGGACCGCGGAAAATTCGGTCCCGTCTTATGTGCGGACTCACCCGCTGACCTCCGAGCGGATTGCCGACATGCAGGACCGCGTCAGCCATGCCAGCAAGCGCAAGGT  <  GWNJ‑0478:712:GW2002102894th:2:2214:3584:44429/150‑1 (MQ=60)
                                                                                                                                      |                                                                                                                                                  
GACGCCGCGGCGGCGCTGGCCATGGGCGGGCAGGGCGCGGCCATCGCCAACCAGCTGTCGTTCTCGCGCGGGGCCGAGCGCGAGGCCGACCGGGTCGGCTTCCAGATCCTGACCGCGGCGGGGTTTGACCCGCATGGCATGCCCGATTTCTTCATGCGGCTGCAGCGCGCATCGGGGACCGCGGAAAATTCGGTCCCGTCTTATGTGCGGACTCACCCGCTGACCTCCGAGCGGATTGCCGACATGCAGGACCGCGTCAGCCATGCCAGCAAGCGCAAGGT  >  AM260479/582455‑582735

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑