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
A3 F50 I2 R1 193 39.9 1341687 91.8% 1231668 149.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,432,298 A→G T1084A (ACG→GCG)  stfR → Rac prophage; putative tail fiber protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,432,2980AG100.0% 96.6 / NA 26T1084A (ACG→GCG) stfRRac prophage; putative tail fiber protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (20/6);  total (20/6)

GCTGGTAGTGCATCAACAAGATTGTCTGTTGTGCATAATCAAAACTATGCAACATCATCTGCTGGCGCACATACCCACTCACTGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCGCATACTGTCGGTATTGGTGCTCATACGCACTCCGTTGCGATTGGTTCACATGGACACACCATCACCGTTAACGCTGCTGGTAACGCGGAAAACACCGTCAAAAACATCGCATTTAACTATATTGTGAGGCTTGCATAATGG  >  NC_000913/1432157‑1432414
                                                                                                                                             |                                                                                                                    
gCTGGTAGTGCATCAACAAGATTGTCTGTTGTGCATAATCAAAACTATGCAACATCATCTGCTGGCGCACATACCCACTCACTGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCGCATACTGTCGGTATTGGTGCTCATGCGCACTcc                                                                                                              <  2:324846/150‑1 (MQ=255)
        tGCATCAACAAGATTGTCTGTTGTGCATAATCAAAACTATGCAACATCATCTGCTGGCGCACATACCCACTCACTGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCGCATACTGTCGGTATTGGTGCTCATGCGCACTCCGTTGCGAtt                                                                                                     >  2:286939/1‑151 (MQ=255)
                caaGATTGTCTGTTGTGCATAATCAAAACTATGCAACATCATCTGCTGGCGCACATACCCACTCACTGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCGCATACTGTCGGTATTGGTGCTCATGCGCACTCCGTTGCGATTGGTTcac                                                                                              >  1:653016/1‑150 (MQ=255)
                 aaGATTGTCTGTTGTGCATAATCAAAACTATGCAACATCATCTGCTGGCGCACATACCCACTCACTGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCGCATACTGTCGGTATTGGTGCTCATGCGCACTCCGTTGCGATTGGTTCACAt                                                                                            >  2:576104/1‑151 (MQ=255)
                    aTTGTCTGTTGTGCATAATCAAAACTATGCAACATCATCTGCTGGCGCACATACCCACTCACTGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCGCATACTGTCGGTATTGGTGCTCATGCGCACTCCGTTGCGATTGGTTCACATgg                                                                                          >  2:177487/1‑150 (MQ=255)
                                   tagtCAAAACTATGCAACATCATCTGCTGGCGCACATACCCACTCACTGTCCGGCACTGCTGCAAGCGCAGGGGCACACGCGCATACTGTCGGTATTGGTGCTCATGCGCACTCCGTTGCGATTGGTTCACATGGACACACCATCACCGtt                                                                          >  2:240882/4‑151 (MQ=255)
                                    aaTCAAAACTATGCAACATCATCTGCTGGCGCACATACCCACTCACTGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCGCATACTGTCGGTATTGGTGCTCATGCGCACTCCGTTGCGATTGGTTCACATGGACACACCATCACCGtt                                                                          >  1:489375/1‑150 (MQ=255)
                                      tCAAAACTATGCAACATCATCTGCTGGCGCACATACCCACTCACTGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCGCATACTGTCGGTATTGGTGCTCATGCGCACTCCGTTGCGATTGGTTCACATGGACACACCATCACCGTTAAc                                                                       >  2:435983/1‑151 (MQ=255)
                                            cTATGCAACATCATCTGCTGGCGCACATACCCACTCACTGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCGCATACTGTCGGTATTGGTGCTCATGCGCACTCCGTTGCGATTGGTTCACATGGACACACCATCACCGTTAACgctgct                                                                 >  1:276631/1‑151 (MQ=255)
                                              aTGCAACATCATCTGCTGGCGCACATACCCACTCACTGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCGCATACTGTCGGTATTGGTGCTCATGCGCACTCCGTTGCGATTGGTTCACATGGACACACCATCACCGTTAACGCTGCTgg                                                               >  2:307592/1‑151 (MQ=255)
                                                   aCATCATCTGCTGGCGCACATACCCACTCACTGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCGCATACTGTCGGTATTGGTGCTCATGCGCACTCCGTTGCGATTGGTTCACATGGACACACCATCACCGTTAACGCTGCTGGTAAcg                                                          <  2:596685/151‑1 (MQ=255)
                                                   aCATCATCTGCTGGCGCACATACCCACTCACTGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCGCATACTGTCGGTATTGGTGCTCATGCGCACTCCGTTGCGATTGGTTCACATGGACACACCATCACCGTTAACGCTGCTGGTAAcg                                                          >  2:290184/1‑151 (MQ=255)
                                                                    acaTACCCACTCACTGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCGCATACTGTCGGTATTGGTGCTCATGCGCACTCCGTTGCGATTGGTTCACATGGACACACCATCACCGTTAACGCTGCTGGTAACGCGGAAAACACCGTCaa                                          >  1:351569/1‑150 (MQ=255)
                                                                     caTACCCACTCACTGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCGCATACTGTCGGTATTGGTGCTCATGCGCACTCCGTTGCGATTGGTTCACATGGACACACCATCACCGTTAACGCTGCTGGTAACGCGGAAAACACCGTCaaa                                         >  1:498801/1‑150 (MQ=255)
                                                                       tACCCACTCACTGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCGCATACTGTCGGTATTGGTGCTCATGCGCACTCCGTTGCGATTGGTTCACATGGACACACCATCACCGTTAACGCTGCTGGTAACGCGGAAAACACCGTCaaaaa                                       >  1:200194/1‑150 (MQ=255)
                                                                              tcactGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCGCATACTGTCGGTATTGGTGCTCATGCGCACTCCGTTGCGATTGGTTCACATGGACACACCATCACCGTTAACGCTGCTGGTAACGCGGAAAACACCGTCAAAAACATCGCAt                               >  1:350138/1‑151 (MQ=255)
                                                                               cactGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCGCATACTGTCGGTATTGGTGCTCATGCGCACTCCGTTGCGATTGGTTCACATGGACACACCATCACCGTTAACGCTGCTGGTAACGCGGAAAACACCGTCAAAAACATCGCAtt                              >  2:598787/1‑151 (MQ=255)
                                                                                            tgctgcAAGCGCAGGTGCACACGCGCATACTGTCGGTATTGGTGCTCATGCGCACTCCGTTGCGATTGGTTCACATGGACACACCATCACCGTTAACGCTGCTGGTAACGCGGAAAACACCGTCAAAAACATCGCATTTAACTATATtgtg                 >  1:101713/1‑151 (MQ=38)
                                                                                             gctgcAAGCGCAGGTGCACACGCGCATACTGTCGGTATTGGTGCTCATGCGCACTCCGTTGCGATTGGTTCACATGGACACACCATCACCGTTAACGCTGCTGGTAACGCGGAAAACACCGTCAAAAACATCGCATTTAACTATATtgtg                 <  2:467954/150‑1 (MQ=38)
                                                                                                gcAAGCGCAGGTGCACACGCGCATACTGTCGGTATTGGTGCTCATGCGCACTCCGTTGCGATTGGTTCACATGGACACACCATCACCGTTAACGCTGCTGGTAACGCGGAAAACACCGTCAAAAACATCGCATTTAACTATATTGTGAg               <  1:175775/149‑1 (MQ=38)
                                                                                                 cAAGCGCAGGTGCACACGCGCATACTGTCGGTATTGGTGCTCATGCGCACTCCGTTGCGATTGGTTCACATGGACACACCATCACCGTTAACGCTGCTGGTAACGCGGAAAACACCGTCAAAAACATCGCATTTAACTATATTGTGAGGCt            >  1:657940/1‑151 (MQ=38)
                                                                                                      gcAGGTGCACACGCGCATACTGTCGGTATTGGTGCTCATGCGCACTCCGTTGCGATTGGTTCACATGGACACACCATCACCGTTAACGCTGCTGGTAACGCGGAAAACACCGTCAAAAACATCGCATTTAACTATATTGTGAGGCTTGCAt       >  2:303729/1‑151 (MQ=38)
                                                                                                      gcAGGTGCACACGCGCATACTGTCGGTATTGGTGCTCATGCGCACTCCGTTGCGATTGGTTCACATGGACACACCATCACCGTTAACGCTGCTGGTAACGCGGAAAACACCGTCAAAAACATCGCATTTAACTATATTGTGAGGCTTGCAt       >  2:389696/1‑151 (MQ=38)
                                                                                                      gcAGGTGCACACGCGCATACTGTCGGTATTGGTGCTCATGCGCACTCCGTTGCGATTGGTTCACATGGACACACCATCACCGTTAACGCTGCTGGTAACGCGGAAAACACCGTCAAAAACATCGCATTTAACTATATTGTGAGGCTTGCAt       >  2:504554/1‑151 (MQ=38)
                                                                                                       cAGGTGCACACGCGCATACTGTCGGTATTGGTGCTCATGCGCACTCCGTTGCGATTGGTTCACATGGACACACCATCACCGTTAACGCTGCTGGTAACGCGGAAAACACCGTCAAAAACATCGCATTTAACTATATTGTGAGGCTTGCATa      <  2:350141/151‑1 (MQ=38)
                                                                                                            gCACACGCGCATACTGTCGGTATTGGTGCTCATGCGCACTCCGTTGCGATTGGTTCACATGGACACACCATCACCGTTAACGCTGCTGGTAACGCGGAAAACACCGTCAAAAACATCGCATTTAACTATATTGTGAGGCTTGCATAATgg  <  1:493874/150‑1 (MQ=25)
                                                                                                                                             |                                                                                                                    
GCTGGTAGTGCATCAACAAGATTGTCTGTTGTGCATAATCAAAACTATGCAACATCATCTGCTGGCGCACATACCCACTCACTGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCGCATACTGTCGGTATTGGTGCTCATACGCACTCCGTTGCGATTGGTTCACATGGACACACCATCACCGTTAACGCTGCTGGTAACGCGGAAAACACCGTCAAAAACATCGCATTTAACTATATTGTGAGGCTTGCATAATGG  >  NC_000913/1432157‑1432414

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A