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 F2 I195 R1 222 27.1 1551108 96.0% 1489063 86.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NZ_CP009273 2,614,493 T→C intergenic (‑262/‑63) upp ← / → purM uracil phosphoribosyltransferase/phosphoribosylformylglycinamidine cyclo‑ligase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092732,614,4930TC100.0% 38.2 / NA 12intergenic (‑262/‑63)upp/purMuracil phosphoribosyltransferase/phosphoribosylformylglycinamidine cyclo‑ligase
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (7/5);  total (7/5)

TACCCTGGCACAAGTCTTCTTTCGCCGCGCGCCTGGGGAAAAGACGTGCAAAAAGGTTGTGTAAAGCAGTCTCGCAAACGTTTGCTTTCCCTGTTAGAATTGCGCCGAATTTTATTTTTCTACCGCAAGTAACGCGTGGGGACCCAAGCAGTGACCGATAAAA  >  NZ_CP009273/2614406‑2614568
                                                                                       |                                                                           
tACCCTGGCACAAGTCTTCTTTCGCCGCGCGCCTGGGGAAAAGACGTGCAAAAAGGTTGTGTAAAGCAGTCTCGCAAACGTTTGCTTccc                                                                           <  2:203720/90‑1 (MQ=255)
tACCCTGGCACAAGTCTTCTTTCGCCGCGCGCCTGGGGAAAAGACGTGCAAAAAGGTTGTGTAAAGCAGTCTCGCAAACGTTTGCTTccc                                                                           <  2:668999/90‑1 (MQ=255)
          caAGTCTTCTTTCGCCGCGCGCCTGGGGAAAAGACGTGCAAAAAGGTTGTGTAAAGCAGTCTCGCAAACGTTTGCTTCCCCTGTTAGAAt                                                                 <  1:645080/90‑1 (MQ=255)
            aGTCTTCTTTCGCCGCGCGCCTGGGGAAAAGACGTGCAAAAAGGTTGTGTAAAGCAGTCTCGCAAACGTTTGCTTCCCCTGTTAGAATTg                                                               >  2:409796/1‑90 (MQ=255)
                ttcttTCGCCGCGCGCCTGGGGAAAAGACGTGCAAAAAGGTTGTGTAAAGCAGTCTCGCAAACGTTTGCTTCCCCTGTTAGAATTGCGcc                                                           <  1:282479/90‑1 (MQ=255)
                       gccgcGCGCCTGGGGAAAAGACGTGCAAAAAGGTTGTGTAAAGCAGTCTCGCAAACGTTTGCTTCCCCTGTTAGAATTGCGCCGAatttt                                                    >  2:82891/1‑90 (MQ=255)
                                                   aaaGGTTGTGTAAAGCAGTCTCGCAAACGTTTGCTTCCCCTGTTAGAATTGCGCCGAATTTTATTTTTCTACCGCAAGTAACGCGTgggg                        <  2:619565/90‑1 (MQ=255)
                                                         tgtgTAAAGCAGTCTCGCAAACGTTTGCTTCCCCTGTTAGAATTGCGCCGAATTTTATTTTTCTACCGCAAGTAACGCGTGGGGACCCaa                  >  1:186230/1‑90 (MQ=255)
                                                         tgtgTAAAGCAGTCTCGCAAACGTTTGCTTCCCCTGTTAGAATTGCGCCGAATTTTATTTTTCTACCGCAAGCAACGCTTGGGGACCCaa                  >  1:388723/1‑90 (MQ=255)
                                                                aGCAGTCTCGCAAACGTTTGCTTCCCCTGTTAGAATTGCGCCGAATTTTATTTTTCTACCGCAAGTAACGCGTGGGGACCCAAGCAg              <  1:239652/87‑1 (MQ=255)
                                                                aGCAGTCTCGCAAACGTTTGCTTCCCCTGTTAGAATTGCGCCGAATTTTATTTTTCTACCGCAAGTAACGCGTGGGGACCCAAGCAg              >  2:239652/1‑87 (MQ=255)
                                                                    gTCTCGCAAACGTTTGCTTCCCCTGTTAGAATTGCGCCGAATTTTATTTTTCTACCGCAAGTAACGCGTGGGGACCCAAGCAGTGACCGa       >  2:575592/1‑90 (MQ=255)
                                                                      ctcGCAAACGTTTGCTTCCCCTGTTAGAATTGCGCCGAATTTTATTTTTCTACCGCAAGTAACGCGTGGGGACCCAAGCAGTGACCGATa     >  2:59831/1‑90 (MQ=255)
                                                                         gCAAACGTTTGCTTCCCCTGTTAGAATTGCGCCGAATTTTATTTTTCTACCGCAAGTAACGCGTGGGGACCCAAGCAGTGACCGATaaaa  <  2:96877/90‑1 (MQ=255)
                                                                                       |                                                                           
TACCCTGGCACAAGTCTTCTTTCGCCGCGCGCCTGGGGAAAAGACGTGCAAAAAGGTTGTGTAAAGCAGTCTCGCAAACGTTTGCTTTCCCTGTTAGAATTGCGCCGAATTTTATTTTTCTACCGCAAGTAACGCGTGGGGACCCAAGCAGTGACCGATAAAA  >  NZ_CP009273/2614406‑2614568

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

BRESEQ :: bam2aln output
AAAACTAACCTTTACCCTGGCACAAGTCTTCTTTCGCCGCGCGCCTGGGGAAAAGACGTGCAAAAAGGTTGTGTAAAGCAGTCTCGCAAACGTTTGCTTTCCCTGTTAGAATTGCGCCGAATTTTATTTTTCTACCGCAAGTAACGCGTGGGGACCCAAGCAGTGACCGATAA  >  NZ_CP009273/2614394‑2614566
                                                                                                   |                                                                         
AAAACTAACCTTTACCCTGGCACAAGTCTTCTTTCGCCGCGCGCCTGGGGAAAAGACGTGCAAAAAGGTTGTGTAAAGCAGTCTCGCAAACGTTTGCTTC                                                                           >  SRR3722073.532684/1‑100 (MQ=60)
                      CAAGTCTTCTTTCGCCGCGCGCCTGGGGAAAAGACGTGCAAAAAGGTTGTGTAAAGCAGTCTCGCAAACGTTTGCTTCCCCTGTTAGAATTGCGCCGAAT                                                     <  SRR3722073.658371/100‑1 (MQ=60)
                            TTCTTTCGCCGCGCGCCTGGGGAAAAGACGTGCAAAAAGGTTGTGTAAAGCAGTCTCGCAAACGTTTGCTTCCCCTGTTAGAATTGCGCCGAATTTTATT                                               <  SRR3722073.288459/100‑1 (MQ=60)
                                                           GCAAAAAGGTTGTGTAAAGCAGTCTCGCAAACGTTTGCTTCCCCTGTTAGAATTGCGCCGAATTTTATTTTTCTACCGCAAGTAACGCGTGGGGACCCAA                >  SRR3722073.189878/1‑100 (MQ=60)
                                                           GCAAAAAGGTTGTGTAAAGCAGTCTCGCAAACGTTTGCTTCCCCTGTTAGAATTGCGCCGAATTTTATTTTTCTACCGCAAGCAACGCTTGGGGACCCAA                >  SRR3722073.397001/1‑100 (MQ=60)
                                                                         TAAAGCAGTCTCGCAAACGTTTGCTTCCCCTGTTAGAATTGCGCCGAATTTTATTTTTCTACCGCAAGTAACGCGTGGGGACCCAAGCAGTGACCGATAA  <  SRR3722073.244673/100‑1 (MQ=60)
                                                                                                   |                                                                         
AAAACTAACCTTTACCCTGGCACAAGTCTTCTTTCGCCGCGCGCCTGGGGAAAAGACGTGCAAAAAGGTTGTGTAAAGCAGTCTCGCAAACGTTTGCTTTCCCTGTTAGAATTGCGCCGAATTTTATTTTTCTACCGCAAGTAACGCGTGGGGACCCAAGCAGTGACCGATAA  >  NZ_CP009273/2614394‑2614566

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑