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
A7 F1 I2 R1 94 59.5 3027142 91.9% 2781943 108.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,677,937 T→C intergenic (‑34/‑490) pntA ← / → ydgH pyridine nucleotide transhydrogenase, alpha subunit/DUF1471 family periplasmic protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,677,9370TC100.0% 192.2 / NA 52intergenic (‑34/‑490)pntA/ydgHpyridine nucleotide transhydrogenase, alpha subunit/DUF1471 family periplasmic protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (29/23);  total (29/23)

CGGTAAAACCCAGTTTCAGCAGCTGTTCCACTGTTTTTGGCGTTGCTGCAACACGGGTTTCATTGGTTAACCGTTCTCTTGGTATGCCAATTCGCATGATATTCCCTTCCATCGGTTTTATTGATGATGGTTTGCCTGTGTCAGGAGCCACACAAGCTGCTCATGTACGAGCTAAATGTTACTCCGTTAAAATAAATTAGTAACAAACGCCCTATAACGTACTGAAAATTATGCCTGTGATCTAGCGCCAAAAAT  >  NC_000913/1677807‑1678061
                                                                                                                                  |                                                                                                                            
cGGTAAAACCCAGTTTCAGCAGCTGTTCCACTGTTTTTGGCGTTGCTGCAACACGGGTTTCATTGGTTAACCGTTCTCTTGGTATGCCAATTCGCATGATATTCCCTTCCATCGGTTTTATTGATGATGGCTTGCCtgt                                                                                                                      >  1:358737/1‑139 (MQ=255)
  gTAAAACCCAGTTTCAGCAGCTGTTCCACTGTTTTTGGCGTTGCTGCAACACGGGTTTCATTGGTTAACCGTTCTCTTGGTATGCCAATTCGCATGATATTCCCTTCCATCGGTTTTATTGATGATGGCTTGCCTgtgt                                                                                                                    >  1:1010531/1‑139 (MQ=255)
          cAGTTTCAGCAGCTGTTCCACTG‑TTTTGGCGTTGCTGCAACACGGGTTTCATTGGTTAACCGTTCTCTTGGTATGCCAATTCGCATGATATTCCCTTCCATCGGTTTTATTGATGATGGCTTGCCTGTGTc                                                                                                                   >  2:162901/1‑131 (MQ=255)
          cAGTTTCAGCAGCTGTTCCACTG‑TTTTGGCGTTGCTGCAACACGGGTTTCATTGGTTAACCGTTCTCTTGGTATGCCAATTCGCATGATATTCCCTTCCATCGGTTTTATTGATGATGGCTTGCCTGTGTc                                                                                                                   <  1:162901/131‑1 (MQ=255)
                 agcagcTGTTCCACTGTTTTTGGCGTTGCTGCAACACGGGTTTCATTGGTTAACCGTTCTCTTGGTATGCCAATTCGCATGATATTCCCTTCCATCGGTTTTATTGATGATGGCTTGCCTGTGTCAGGAGCCACACAAg                                                                                                     <  2:1503065/139‑1 (MQ=255)
                 agcagcTGTTCCACTGTTTTTGGCGTTGCTGCAACACGGGTTTCATTGGTTAACCGTTCTCTTGGTATGCCAATTCGCATGATATTCCCTTCCATCGGTTTTATTGATGATGGCTTGCCTGTGTCAGGAGCCACACAAg                                                                                                     >  1:670504/1‑139 (MQ=255)
                       tGTTCCACTGTTTTTGGCGTTGCTGCAACACGGGTTTCATTGGTTAACCGTTCTCTTGGTATGCCAATTCGCATGATATTCCCTTCCATCGGTTTTATTGATGATGGCTTGCCTGTGTCAGGAGCCACACAAGCTGCTc                                                                                               >  2:516339/1‑139 (MQ=255)
                       tGTTCCACTGTTTTTGGCGTTGCTGCAACACGGGTTTCATTGGTTAACCGTTCTCTTGGTATGCCAATTCGCATGATATTCCCTTCCATCGGTTTTATTGATGATGGCTTGCCTGTGTCAGGAGCCACACAAGCTGCTc                                                                                               >  1:902496/1‑139 (MQ=255)
                             aCTGTTTTTGGCGTTGCTGCAACACGGGTTTCATTGGTTAACCGTTCTCTTGGTATGCCAATTCGCATGATATTCCCTTCCATCGGTTTTATTGATGATGGCTTGCCTGTGTCAGGAGCCACACAAGCTGCTCATGTAc                                                                                         <  1:156609/139‑1 (MQ=255)
                             aCTGTTTTTGGCGTTGCTGCAACACGGGTTTCATTGGTTAACCGTTCTCTTGGTATGCCAATTCGCATGATATTCCCTTCCATCGGTTTTATTGATGATGGCTTGCCTGTGTCAGGAGCCACACAAGCTGCTCATGTAc                                                                                         <  1:516339/139‑1 (MQ=255)
                                  ttttGGCGTTGCTGCAACACGGGTTTCATTGGTTAACCGTTCTCTTGGTATGCCAATTCGCATGATATTCCCTTCCATCGGTTTTATTGATGATGGCTTGCCTGTGTCAGGAGCCACACAAGCTGCTCATGTACGAGCt                                                                                    <  2:670504/139‑1 (MQ=255)
                                   tttGGCGTTGCTGCAACACGGGTTTCATTGGTTAACCGTTCTCTTGGTATGCCAATTCGCATGATATTCCCTTCCATCGGTTTTATTGATGATGGCTTGCCTGTGTCAGGAGCCACACAAGCTGCTCATGTACGAGCTa                                                                                   >  2:1163075/1‑139 (MQ=255)
                                                cAACACGGGTTTCATTGGTTAACCGTTCTCTTGGTATGCCAATTCGCATGATATTCCCTTCCATCGGTTTTATTGATGATGGCTTGCCTGTGTCAGGAGCCACACAAGCTGCTCATGTAAGAGCTAAATGTTACTCCGt                                                                      <  2:358737/139‑1 (MQ=255)
                                                         tttCATTGGTTAACCGTTCTCTTGGTATGCCAATTCGCATGATATTCCCTTCCATCGGTTTTATTGATGATGGCTTGCCTGTGTCAGGAGCCACACAAGCTGCTCATGTACGAGCTAAATGTTACTCCGTTAaaataaa                                                             <  2:1010531/139‑1 (MQ=255)
                                                                 gTTAACCGTTCTCTTGGTATGCCAATTCGCATGATATTCCCTTCCATCGGTTTTATTGATGATGGCTTGCCTGTGTCAGGAGCCACACAAGCTGCTCATGTACGAGCT‑‑ATGTTACTCCGTTAAAATAAATTAGTAACaa                                                   <  1:814081/139‑1 (MQ=255)
                                                                   tAACCGTTCTCTTGGTATGCCAATTCGCATGATATTCCCTTCCATCGGTTTTATTGATGATGGCTTGCCTGTGTCAGGAGCCACACAAGCTGCTCATGTACGAGCTAAATGTTACTCCGTTAAAATAAATTAGTAACaa                                                   >  1:618124/1‑139 (MQ=255)
                                                                    aaCCGTTCTCTTGGTATGCCAATTCGCATGATATTCCCTTCCATCGGTTTTATTGATGATGGCTTGCCTGTGTCAGGAGCCACACAAGCTGCTCATGTACGAGCTAAATGTTACTCCGTTAAAATAAATTAGTAACaaa                                                  >  2:681228/1‑139 (MQ=255)
                                                                    aaCCGTTCTCTTGGTATGCCAATTCGCATGATATTCCCTTCCATCGGTTTTATTGATGATGGCTTGCCTGTGTCAGGAGCCACACAAGCTGCTCATGTACGAGCTAAATGTTACTCCGTTAAAATAAATTAGTAACaaa                                                  <  2:902496/139‑1 (MQ=255)
                                                                     aCCGTTCTCTTGGTATGCCAATTCGCATGATATTCCCTTCCATCGGTTTTATTGATGATGGCTTGCCTGTGTCAGGAGCCACACAAGCTGCTCATGTACGAGCTAAATGTTACTCCGTTAAAATAAATTAGTAACAAAc                                                 <  2:618124/139‑1 (MQ=255)
                                                                      aggTTCTCTTGGTATGCCAATTCGGATTATATTCCCTGCCATCGGTTTTATTGATGATGGCTTGCCTGTGTCAGGAGCCACACAAGCTGCTAATGTACGAGCTTAATGTTACTCCGTTAAAATAAATTAGTAACAAACg                                                <  2:1130555/137‑1 (MQ=255)
                                                                         ttCTCTTGGTACGCCAATTCGCATGATATTCCCTTCCATCGGTTTTATTGATGATGGCTTGCCTGTGTCAGGAGCCACACAAGCTGCTCATGTACGAGCTAAATGTTACTCCGTTAAAATAAATTAGTAACaaa                                                  >  1:358911/1‑134 (MQ=255)
                                                                         ttCTCTTGGTACGCCAATTCGCATGATATTCCCTTCCATCGGTTTTATTGATGATGGCTTGCCTGTGTCAGGAGCCACACAAGCTGCTCATGTACGAGCTAAATGTTACTCCGTTAAAATAAATTAGTAACaaa                                                  <  2:358911/134‑1 (MQ=255)
                                                                           ctctTGGTATGCCAATTCGCATGTTATTCCCTTCCATCGGTTTTATTGATGATGGCTTGCCTGTGTCAGGAGCCACACAAGCTGCTCATGTACGAGCTAAATGTTACTCCGTTAAAATAAATTAGTAACAAACGCCCta                                           >  2:269420/1‑139 (MQ=255)
                                                                              ttGGTATGCCAATTCGCATGATATTCCCTTCCATCGGTTATATTGATGATGGCTTGCCTGTGTCAGGAGCCACACAAGCTGCTCATGTACGAGCTAAATGTTACTCCGTTAAAATAAATTAGTAACAAACGCCCTATaa                                        >  1:184537/1‑139 (MQ=255)
                                                                                ggTATGCCAATTCGCATGATATTCCCTTCCATCGGTTTTATTGATGATGGCTTGCCTGTGTCAGGAGCCACACAAGCTGCTCATGTACGAGCTAAATGTTACTCCGTTAAAATAAATTAGTAACAAACGCCCTATAACg                                      >  1:1276178/1‑139 (MQ=255)
                                                                                   aTGCCAATTCGCATGATATTCCCTTCCATCGGTTTTATTGATGATGGCTTGCCTGTGTCAGGAGCCACACAATCTGCTCATGTACGAGCTTAATGTTACTCCGTTAAAATAAATTAGTAACAAACGCCCTATAACGtct                                   >  1:1130555/1‑137 (MQ=255)
                                                                                        aaTTCGCATGATATTCCCTTCCATCGGTTTTATTGATGATGGCTTGCCTGTGTCAGGAGCCACACAAg                                                                                                     <  1:30525/68‑1 (MQ=255)
                                                                                        aaTTCGCATGATATTCCCTTCCATCGGTTTTATTGATGATGGCTTGCCTGTGTCAGGAGCCACACAAg                                                                                                     >  2:30525/1‑68 (MQ=255)
                                                                                          ttCGCATGATATTCCCTTCCATCGGTTTTATTGATGATGGCTTGCCTGTGTCAGGAGCCACACAAGCTGCTCATGTACGAGCTAAATGTTACTCCGTTAAAATAAATTAGTAACAAACGCCCTATAACGTACTGAAAAt                            >  2:794554/1‑139 (MQ=255)
                                                                                           tCGCATGATATTCCCTTCCATCGGTTTTATTGATGATGGCTTGCCTGTGTCAGGAGCCACACAAg                                                                                                     <  2:643767/65‑1 (MQ=255)
                                                                                           tCGCATGATATTCCCTTCCATCGGTTTTATTGATGATGGCTTGCCTGTGTCAGGAGCCACACAAg                                                                                                     >  1:643767/1‑65 (MQ=255)
                                                                                             gCATGATATTCCCTTCCATCGGTTTTATTGATGATGGCTTGCCTGTGTCAGGAGCCACACAAGCTGCTCATGTACGAGCTAAATGTTACTCCGTTAAAATAAATTAGTAACAAACGCCCTATAACGTACTGAAAATTAt                         <  1:794554/139‑1 (MQ=255)
                                                                                              cATGATATTCCCTTCCATCGGTTTTATTGATGATGGCTTGCCTGTGTCAGGAGCCACACAAGCTGCTCATGTACGAGCTAAATGTTACTCCGTTAAAATAAATTAGTAACAAACGCCCTATAACGTACTGAAAATTATg                        >  1:328031/1‑139 (MQ=255)
                                                                                                  atatTCCCTTCCATCGGTTTTATTGATGATGGCTTGCCTGTGTCAGGAGCCACACAAg                                                                                                     <  1:1089029/58‑1 (MQ=255)
                                                                                                  atatTCCCTTCCATCGGTTTTATTGATGATGGCTTGCCTGTGTCAGGAGCCACACAAg                                                                                                     >  2:1089029/1‑58 (MQ=255)
                                                                                                           tCCATCGGTTTTATTGATGATGGCTTGCCTGTGTCAGGAGCCACACAAGCTGCTCATGTACGAGCTAAATGTTACTCCGTTAAAATAAATTAGTAACAAACGCCCtata                                         >  1:376477/1‑109 (MQ=255)
                                                                                                           tCCATCGGTTTTATTGATGATGGCTTGCCTGTGTCAGGAGCCACACAAGCTGCTCATGTACGAGCTAAATGTTACTCCGTTAAAATAAATTAGTAACAAACGCCCtata                                         <  2:376477/109‑1 (MQ=255)
                                                                                                            ccATCGGTTTTATTGATGATGGCTTGCCTGTGTCAGGAGCCACACAAGCTGCTCATGTACGAGCTAAATGTTACTCCGTTAAAATAAATTAGTAACAAACGCCCTATAACGTACTGAAAATTATGCCTGTGATCTAgcg          >  2:349335/1‑139 (MQ=255)
                                                                                                             cATCGGTTTTATTGATGATGGCTTGCCTGTGTCAGGAGCCACACAAGCTGCTCTTGTACGAGCTAAATGTTACTCCGTTAAAATAAATTAGTAACAAACGCCCTATAACGTACTTAAAATTATGCCTGTGATCTAgcgc         >  1:841355/1‑139 (MQ=255)
                                                                                                             cATCGGTTTTATTGATGATGGCTTGCCTGTGTCAGGAGCCACACAAGCTGCTCATGTACGAGCt                                                                                    >  2:887742/1‑64 (MQ=255)
                                                                                                             cATCGGTTTTATTGATGATGGCTTGCCTGTGTCAGGAGCCACACAAGCTGCTCATGTACGAGCt                                                                                    <  1:887742/64‑1 (MQ=255)
                                                                                                             cATCGGTTTTATTGATGATGGCTTGCCTGTGTCAGGAGCCACACAAGCTGCTCATGTACGAGCTAAATGTTACTCCGTTAAAATAAATTAGTAACAAACGCCCTATAACGTACTGAAAATTATGCCTGTGATCTAgcgc         >  1:22401/1‑139 (MQ=255)
                                                                                                               tCGGTTTTATTGATGATGGCTTGCCTGTGTCAGGAGCCACACAAGCTGCTCATGTACGAGCTAAATGTTACTCCGTTAAAATAAATTAGTAACAAACGCCCTATAACGTACTGAAAATTATGCCTGTGATCTAGCGCCa       >  2:1411125/1‑139 (MQ=255)
                                                                                                                cGGTTTTATTGATGATGGCTTGCCTGTGTCAGGAGCCACACAAGCTGCTCATGTACGAGCTAAATGTTACTCCGTTAAAATAAATTAGTAACAAACGCCCTATAACGTACTg                                 <  1:885655/112‑1 (MQ=255)
                                                                                                                cGGTTTTATTGATGATGGCTGGCCTGTGTCAGGAGCCACACAAGCTGCTCATGTACGAGCTAAATGTTACTCCGTTAAAATAAATTAGTAACAAACGCCCTATAACGTACTg                                 >  2:885655/1‑112 (MQ=255)
                                                                                                                  gTTTTATTGATGATGGCTTGCCTGTGTCAGGAGCCACACAAGCTGCTCATGTACGAGCTAAATGTTACTCCGTTAAAATAAATTAGTAACAAACGCCCTATAACGTACTGAAAATTATGCCTGTGATCTAGCGCCaaaa    >  2:1033368/1‑139 (MQ=255)
                                                                                                                  gTTTTATTGATGATGGCTTGCCTGTGTCAGGAGCCACACAAGCTGCTCATGTACGAGCTAAATGTTACTCCGTTAAAATAAATTAGTAACAAACGCCCTATAACGTACTGAAAATTATGCCTGTGATCTAGCGCCaaaa    >  2:1054622/1‑139 (MQ=255)
                                                                                                                  gTTTTATTGATGATGGCTTGCCTGTGTCAGGAGCCACACAAGCTGCTCATGTACGAGCTAAATGTTACTCCGTTAAAATAAATTAGTAACAAACGCCCTATAACGTACTGAAAATTATGCCTGTGATCTAGCGCCaaaa    <  1:269420/139‑1 (MQ=255)
                                                                                                                    tttATTGATGATGGCTTGCCTGTGTCAGGAGCCACACAAGCTGCTCTTGTACGAGCTAAATGTTACTCCGTTAAAATAAATTAGTAACAAACGCCCTATAACGTACTGAAAATTATGCCTGTGATCTAGCGCCAAAAAt  <  2:841355/139‑1 (MQ=255)
                                                                                                                    tttATTGATGATGGCTTGCCTGTGTCAGGAGCCACACAAGCTGCTCATGTACGAGCTAAATGTTACTCCGTTAAAATAAATTAGTAACAAACGCCCTATAACGTACTGAAAATTATGCCTGTGATCTAGCGCCAAAAAt  <  2:184537/139‑1 (MQ=255)
                                                                                                                             gatgGCTTGCCTGTGTCAGGAGCCACACAAGCTGCTCATGTACGAGCTAAATGTTACTCCGTTAAAATAAATTAGTAAc                                                     >  1:685909/1‑79 (MQ=255)
                                                                                                                             gatgGCTTGCCTGTGTCAGGAGCCACACAAGCTGCTCATGTACGAGCTAAATGTTACTCCGTTAAAATAAATTAGTAAc                                                     <  2:685909/79‑1 (MQ=255)
                                                                                                                                  |                                                                                                                            
CGGTAAAACCCAGTTTCAGCAGCTGTTCCACTGTTTTTGGCGTTGCTGCAACACGGGTTTCATTGGTTAACCGTTCTCTTGGTATGCCAATTCGCATGATATTCCCTTCCATCGGTTTTATTGATGATGGTTTGCCTGTGTCAGGAGCCACACAAGCTGCTCATGTACGAGCTAAATGTTACTCCGTTAAAATAAATTAGTAACAAACGCCCTATAACGTACTGAAAATTATGCCTGTGATCTAGCGCCAAAAAT  >  NC_000913/1677807‑1678061

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