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 152 24.9 2083062 91.6% 1908084 109.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA AM260479 2,579,212 G→C A121A (GCC→GCG)  h16_A2374 ← Metallopeptidase, M23B subfamily

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*AM2604792,579,2120GC100.0% 49.5 / NA 14A121A (GCC→GCG) h16_A2374Metallopeptidase, M23B subfamily
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base C (7/7);  total (7/7)

GACCGGCGCGGCGGCCGCGGCGGGCGCGGCGGGCGTTGCCGCAGGCGCCGAAGCGGCCGCGGCCGGAGGCACCGGCGTGGCGGCCGGGCGGGCCTGGTCGATCGGCTGCGCCTGCACCGTGCCCGGGGCCACCGGCATGGTGGCCACGCCGGGCGCAATGTTGACGTCGGCACCCGGCGGCACGATGCGCAGCAGCTGGCCGACCTCGATCTGGTTCACATTGGTCAGGTTGTT  >  AM260479/2579086‑2579319
                                                                                                                              |                                                                                                           
gACCGGCGCGGCGGCCGCGGCGGGCGCGGCGGGCGTTGCCGCAGGCGCCGAAGCGGCCGCGGCCGGAGGCACCGGCGTGGCGGCCGGGCGGGCCTGGTCGATCGGCTGCGCCTGCACCGTGCCCGGCGCCACCg                                                                                                      >  1:715961/1‑134 (MQ=255)
                                                     cggccgcggccgGAGGCACCGGCGTGGCGGCCGGGCGGGCCTGGTCGATCGGCTGCGCCTGCACCGTGCCCGGCGCCACCGGCATGGTGGCCACGCCGGGCGCAGTGTTGACGTCGGCACCCGGCGGCACGATg                                                 >  1:1027096/1‑134 (MQ=255)
                                                            ggccgGAGGCACCGGCGTGGCGGCCGGGCGGGCCTGGTCGATCGGCTGCGCCTGCACCGTGCCCGGCGCCACCGGCATGGTGGCCACGCCGGGCGCAgtgt                                                                           >  1:806833/1‑101 (MQ=255)
                                                            ggccgGAGGCACCGGCGTGGCGGCCGGGCGGGCCTGGTCGATCGGCTGCGCCTGCACCGTGCCCGGCGCCACCGGCATGGTGGCCACGCCGGGCGCAgtgt                                                                           <  2:806833/101‑1 (MQ=255)
                                                                             tGGCGGCCGGGCGGGCCTGGTCGATCGGCTGCGCCTGCACCGTGCCCGGCGCCACCGGCATGGTGGCCACGCCGGGCGCAGTGTTGACGTCGGCACCCGGCGGCACGATGCGCAGCAGCTGGCCGACCTCGATc                         <  1:665275/134‑1 (MQ=255)
                                                                                  gcCGGGCGGGCCTGGTCGATCGGCTGCGCCTGCACCGTGCCCGGCGCCACCgg                                                                                                     <  1:630906/53‑1 (MQ=255)
                                                                                  gcCGGGCGGGCCTGGTCGATCGGCTGCGCCTGCACCGTGCCCGGCGCCACCgg                                                                                                     >  2:630906/1‑53 (MQ=255)
                                                                                       gcgggcCTGGTCGATCGGCTGCGCCTGCACCGTGCCCGGCGCCACCGGCATGGTGGCCACGCCGGGCGCAGTGTTGACGTCGGCACCCGGCGGCACGATGCGCAGCAGCTGGCCGACCTCGATCTGGTTCACAt               <  2:1027096/134‑1 (MQ=255)
                                                                                                   gATCGGCTGCGCCTGCACCGTGCCCGGCGCCACCGGCATGGTGGCCACGCCGGGCGCAGTGTTGACGTCGGCACCCGGCGGCACGATGCGCAGCAGCTGGCCGACCTCGATCTGGTTCACATTGGTCAGgttgt   <  2:547340/134‑1 (MQ=255)
                                                                                                    aTCGGCTGCGCCTGCACCGTGCCCGGCGCCACCGGCATGGTGGCCACGCCGGGCGCAGTGTTGACGTCGGCACCCGGCGGCACGATGCGCAGCAGCTGGCCGACCTCGATCTGGTTCACATTGGTCAGgttgtt  >  2:172015/1‑134 (MQ=255)
                                                                                                         cTGCGCCTGCACCGTGCCCGGCGCCACCGGCATGGTGGCCACGCCggg                                                                                   >  1:936642/1‑48 (MQ=255)
                                                                                                         cTGCGCCTGCACCGTGCCCGGCGCCACCGGCATGGTGGCCACGCCggg                                                                                   <  2:936642/48‑1 (MQ=255)
                                                                                                                      gTGCCCGGCGCCACCGGCATGGTGGCCACGCCGGGCGCagt                                                                             >  1:734296/1‑39 (MQ=38)
                                                                                                                      gTGCCCGGCGCCACCGGCATGGTGGCCACGCCGGGCGCagt                                                                             <  2:734296/41‑3 (MQ=38)
                                                                                                                              |                                                                                                           
GACCGGCGCGGCGGCCGCGGCGGGCGCGGCGGGCGTTGCCGCAGGCGCCGAAGCGGCCGCGGCCGGAGGCACCGGCGTGGCGGCCGGGCGGGCCTGGTCGATCGGCTGCGCCTGCACCGTGCCCGGGGCCACCGGCATGGTGGCCACGCCGGGCGCAATGTTGACGTCGGCACCCGGCGGCACGATGCGCAGCAGCTGGCCGACCTCGATCTGGTTCACATTGGTCAGGTTGTT  >  AM260479/2579086‑2579319

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ 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
GCCAGCTTCATCGAGCCATCGGTGACCGGCGCGGCGGCCGCGGCGGGCGCGGCGGGCGTTGCCGCAGGCGCCGAAGCGGCCGCGGCCGGAGGCACCGGCGTGGCGGCCGGGCGGGCCTGGTCGATCGGCTGCGCCTGCACCGTGCCCGG‑‑‑GGCCACCGGCAT‑‑‑GGTGGCCACGCCGGGCGCAATGTTGACGTCGGCACCCGGCGGCACGATGCGCAGCAGCTGGCCGACCTCGATCTGGTTCACATTGGTCAGGTTGTTCCACGTTGCCACATCGCG  >  AM260479/2579063‑2579337
                                                                                                                                                        |                                                                                                                                
gaccaggcccgcccggccgccacgccggtgcctcCGGCCGCGGCGGGCGCGGCGGGCGTTGCCGCAGGCGCCGAAGCGGCCGCGGCCGGAGGCACCGGCGTGGCGGCCGGGCGGGCCTGGTCGATCGGCTGCGCCTGCACCGTGCCCGG‑‑‑C                                                                                                                                  >  GWNJ‑0478:712:GW2002102894th:2:2103:11594:72107/35‑150 (MQ=60)
        CATCGAGCCATCGGTGACCGGCGCGGCGGCCGCGGCGGGCGCGGCGGGCGTTGCCGCAGGCGCCGAAGCGGCCGCGGCCGGAGGCACCGGCGTGGCGGCCGGGCGGGCCTGGTCGATCGGCTGCGCCTGCACCGTGCCCGG‑‑‑CGCCACCGG                                                                                                                          >  GWNJ‑0478:712:GW2002102894th:2:2112:12979:49706/1‑150 (MQ=60)
                        caagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagGGCACCGGCGTGGCGGCCGGGCGGGCCTGGTCGATCGGCTGCGCCTGCACCGTGCCCGG‑‑‑CGCCACCGGCAT‑‑‑GGTGGCCACGCC                                                                                                        <  GWNJ‑0478:712:GW2002102894th:2:2108:17581:45664/83‑1 (MQ=60)
                                                             gtGCAGGCGCCGAAGCGGCCGCGGCCGGAGGCACCGGCGTGGCGGCCGGGCGGGCCTGGTCGATCGGCTGCGCCTGCACCGTGCCCGG‑‑‑CGCCACCGGCAT‑‑‑GGTGGCCACGCCGGGCGCAGTGTTGACGTCGGCACCCGGCGGCACGATGC                                                                  >  GWNJ‑0478:712:GW2002102894th:2:2216:4544:24640/3‑150 (MQ=60)
                                                                    CGCCGAAGCGGCCGCGGCCGGAGGCACCGGCGTGGCGGCCGGGCGGGCCTGGTCGATCGGCTGCGCCTGCACCGTGCCCGG‑‑‑CGCCACCGGCAT‑‑‑GGTGGCCACGCCGGGCGCAGTGTTGACGTCGGCACCCGctgtctcttatacacatct                                                           >  GWNJ‑0478:712:GW2002102894th:2:2202:6324:2179/1‑131 (MQ=60)
                                                                                                   GTGGCGGCCGGGCGGGCCTGGTCGATCGGCTGCGCCTGCACCGTGCCCGG‑‑‑CGCCACCGGCAT‑‑‑GGTGGCCACGCCGGGCGCAGTGTTGACGTCGGCACCCGGCGGCACGATGCGCAGCAGCTGGCCGACCTCGATCTGGTTCACATTGGTC                            <  GWNJ‑0478:712:GW2002102894th:2:2111:4127:55893/150‑1 (MQ=60)
                                                                                                                 GGCCTGGTCGATCGGCTGCGCCTGCACCGTGCCCGG‑‑‑CGCCACCGGCAT‑‑‑GGTGGCCACGCCGGGCGCAGTGTTGACGTCctgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttctgcttgaaaaa               >  GWNJ‑0478:712:GW2002102894th:2:2210:20051:27738/1‑78 (MQ=60)
                                                                                                                           ATCGGCTGCGCCTGCACCGTGCCCGGCGTGGCCAC‑‑‑CATGCCGGTGG‑‑‑CGCCGGGCGCAGTGTTGACGTCGGCACCCGGCGGCACGATGCGCAGCAGCTGGCCGACCTCGATCTGGTTCACATTGGTCctgtctcttatgcacatcttccg     >  GWNJ‑0478:712:GW2002102894th:2:1204:1408:76608/1‑126 (MQ=60)
                                                                                                                              GGCTGCGCCTGCACCGTGCCCGG‑‑‑CGCCACCGGCAT‑‑‑GGTGGCCACGCCGGGCGCAGTGTTGACGTCGGCACCCtgtctcttatacacatctccgagcccacgagacggagctacaactcgtatgccgtcttctgcttgaaaaaaaaaaac  >  GWNJ‑0478:712:GW2002102894th:2:2115:12365:52769/1‑72 (MQ=60)
                                                                                                                                                        |                                                                                                                                
GCCAGCTTCATCGAGCCATCGGTGACCGGCGCGGCGGCCGCGGCGGGCGCGGCGGGCGTTGCCGCAGGCGCCGAAGCGGCCGCGGCCGGAGGCACCGGCGTGGCGGCCGGGCGGGCCTGGTCGATCGGCTGCGCCTGCACCGTGCCCGG‑‑‑GGCCACCGGCAT‑‑‑GGTGGCCACGCCGGGCGCAATGTTGACGTCGGCACCCGGCGGCACGATGCGCAGCAGCTGGCCGACCTCGATCTGGTTCACATTGGTCAGGTTGTTCCACGTTGCCACATCGCG  >  AM260479/2579063‑2579337

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑