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
A6 F1 I1 R1 67 31.4 1402038 96.1% 1347358 109.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,904,586 T→C V231A (GTC→GCC)  manZ → mannose‑specific enzyme IID component of PTS

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,904,5860TC100.0% 74.5 / NA 21V231A (GTC→GCC) manZmannose‑specific enzyme IID component of PTS
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (9/12);  total (9/12)

CGTCTATCCTCGGCCTGTTTGTCATGGGGGCATTGGTTAACAAGTGGACACATGTCAACATCCCGCTGGTTGTCTCTCGCATTACTGACCAGACGGGCAAAGAACACGTTACTACTGTCCAGACTATTCTGGACCAGTTAATGCCAGGCCTGGTACCACTGCTGCTGACCTTTGCTTGTATGTGGCTACTGCGCAAAAAAGTTAACCCGCTGTGGATCATCGTTGGCTTCTTCGTCATCGGTATCGCTGGTTA  >  NC_000913/1904469‑1904721
                                                                                                                     |                                                                                                                                       
cGTCTATCCTCGGCCTGTTTGTCATGGGGGCATTGGTTAACAAGTGGACACATGTCAACATCCCGCTGGTTGTCTCTCGCATTACTGACCAGACGGGCAAAGAACACGTTACTACTGCCCAGACTATTCTGGACCAGtt                                                                                                                    <  1:326692/139‑1 (MQ=255)
           ggCCTGTTTGTCATGGGGGCATTGGTTAACAAGTGGACACATGTCAACATCCCGCTGGTTGTCTCTCGCATTACTGACCAGACGGGCAAAGAACACGTTACTACTGCCCAGACTATTCTGGACCAGTTAATGCCAGGcc                                                                                                         <  2:187650/139‑1 (MQ=255)
                                           gTGGACACATGTCAACATCCCGCTGGTTGTCTCTCGCATTACTGACCAGACGGGCAAAGAACACGTTACTACTGCCCAGACTATTCTGGACCAGTTAATGTCAGGCCTGGTACCACTGCTGCTGACCTTTGCTTGTAtg                                                                         >  2:680476/1‑139 (MQ=255)
                                           gTGGACACATGTCAACATCCCGCTGGTTGTCTCTCGCATTACTGACCAGACGGGCAAAGAACACGTTACTACTGCCCAGACTATTCTGGACCAGTTAATGCCAgg                                                                                                           <  2:576054/105‑1 (MQ=255)
                                           gTGGACACATGTCAACATCCCGCTGGTTGTCTCTCGCATTACTGACCAGACGGGCAAAGAACACGTTACTACTGCCCAGACTATTCTGGACCAGTTAATGCCAgg                                                                                                           >  1:576054/1‑105 (MQ=255)
                                             ggACACATGTCAACATCCCGCTGGTTGTCTCTCGCATTACTGACCAGACGGGCAAAGAACACGTTACTACTGCCCAGACTATTCTGGACCAGTTAATGCCAGGCCTGGTACCACTGCTGCTGACCTTTGCTTGTAtgtg                                                                       >  1:187710/1‑139 (MQ=255)
                                              gACACATGTCAACATCCCGCTGGTTGTCTCTCGCATTACTGACCAGACGGGCAAAGAACACGTTACTACTGCCCAGACTATTCTGGa                                                                                                                          <  1:357103/87‑1 (MQ=255)
                                              gACACATGTCAACATCCCGCTGGTTGTCTCTCGCATTACTGACCAGACGGGCAAAGAACACGTTACTACTGCCCAGACTATTCTGGa                                                                                                                          >  2:357103/1‑87 (MQ=255)
                                                     gTCAACATCCCGCTGGTTGTCTCTCGCATTACTGACCAGACGGGCAAAGAACACGTTACTACTGCCCAGACTATTCTGGAc                                                                                                                         <  2:458780/81‑1 (MQ=255)
                                                     gTCAACATCCCGCTGGTTGTCTCTCGCATTACTGACCAGACGGGCAAAGAACACGTTACTACTGCCCAGACTATTCTGGAc                                                                                                                         >  1:458780/1‑81 (MQ=255)
                                                             cccGCTGGTTGTCTCTCGCATTACTGACCAGACGGGCAAAGAACACGTTACTACTGCCCAGACTATTCTGGa                                                                                                                          >  1:156762/1‑72 (MQ=255)
                                                             cccGCTGGTTGTCTCTCGCATTACTGACCAGACGGGCAAAGAACACGTTACTACTGCCCAGACTATTCTGGa                                                                                                                          <  2:156762/72‑1 (MQ=255)
                                                                      tGTCTCTCGCATTACTGACCAGACGGGCAAAGAACACGTTACTACTGCCCAGACTATTCTGGACCAGTTAATGTCAGGCCTGGTACCACTGCTGCTGACCTTTGCTTGTATGTGGCTACTGCGCAAAAAAGTTAACCCg                                              <  1:680476/139‑1 (MQ=255)
                                                                                          aGACGGGCAAAGAACACGTTACTACTGCCCAGACTATTCTGGa                                                                                                                          >  2:417254/1‑43 (MQ=255)
                                                                                          aGACGGGCAAAGAACACGTTACTACTGCCCAGACTATTCTGGa                                                                                                                          <  1:417254/43‑1 (MQ=255)
                                                                                            aCGGGCAAAGAACACGTTACTACTGCCCAGACTATTCTGGACCAGTTAATGCCAGGCCTGGTACCACTGCTGCTGACCt                                                                                    <  1:471715/79‑1 (MQ=255)
                                                                                            aCGGGCAAAGAACACGTTACTACTGCCCAGACTATTCTGGACCAGTTAATGCCAGGCCTGGTACCACTGCTGCTGACCt                                                                                    >  2:471715/1‑79 (MQ=255)
                                                                                               ggCAAAGAACACGTTACTACTGCCCAGACTATTCTGGACCAGTTAATGCCAGGCCTGGTACCACTGCTGCTGACCTTTGc                                                                                <  2:452860/80‑1 (MQ=255)
                                                                                               ggCAAAGAACACGTTACTACTGCCCAGACTATTCTGGACCAGTTAATGCCAGGCCTGGTACCACTGCTGCTGACCTTTGc                                                                                >  1:452860/1‑80 (MQ=255)
                                                                                                   aaGAACACGTTACTACTGCCCAGACTATTCTGGGCCAGTTAATGCCAGGCCTGGTACCTCTGCGGCTGACCTTTGCTTGTATGTGGCTACTGCGCAAAAAAGTTAACCCGCTGTGGAGCATCGTTGGCTTCTTCGTCAt                 <  1:15879/139‑1 (MQ=255)
                                                                                                                  ctGCCCAGACTATTCTGGACCAGTTAATGCCAGGCCTGGTACCACTGCTGCTGACCTTTGCTTGTATGTGGCTACTGCGCAAAAAAGTTAACCCGCTGTGGATCATCGTTGGCTTCTTCGTCATCGGTATCGCTGGTTa  <  2:187710/139‑1 (MQ=255)
                                                                                                                     |                                                                                                                                       
CGTCTATCCTCGGCCTGTTTGTCATGGGGGCATTGGTTAACAAGTGGACACATGTCAACATCCCGCTGGTTGTCTCTCGCATTACTGACCAGACGGGCAAAGAACACGTTACTACTGTCCAGACTATTCTGGACCAGTTAATGCCAGGCCTGGTACCACTGCTGCTGACCTTTGCTTGTATGTGGCTACTGCGCAAAAAAGTTAACCCGCTGTGGATCATCGTTGGCTTCTTCGTCATCGGTATCGCTGGTTA  >  NC_000913/1904469‑1904721

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ 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: ‑

GATK/CNVnator alignment

N/A