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
A19 F106 I0 R1 88 30.3 670850 93.2% 625232 140.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 1,002,200 T→G 100% M173R (ATG→AGG)  mecA2 → competence negative regulator MecA

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007301,002,2000TG100.0% 62.0 / NA 19M173R (ATG→AGG) mecA2competence negative regulator MecA
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base G (8/11);  total (8/11)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

AGGTTCTAAACGTCAAAAGTCTTCAGCACGTAAAAATACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATATGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCAACAGACAGAACAGAAGTTTATTTAAATGACT  >  CP000730/1002063‑1002331
                                                                                                                                         |                                                                                                                                   
aGGTTCTAAACGTCAAAAGTCTTCAGCACGTAAAAATACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGt                                                                                                                                  <  1:250290/141‑1 (MQ=255)
    tCTAAACGTTAAAAGTCTTCAGCACGTAAAAATACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGAt                                                                                                                              <  2:239329/141‑1 (MQ=255)
     cTAAACGTCAAAAGTCTTCAGCACGTAAAAATACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATg                                                                                                                             >  2:317827/1‑141 (MQ=255)
                         gCACGTAAAAATACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGtt                                                                                                         >  2:286816/1‑140 (MQ=255)
                                     agaaggcgaaTCATTGTTAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGt                                                                                             <  2:37292/133‑1 (MQ=255)
                                                    gtgAAACTGAATTATTTAGAAGATGTTATTAATTATGCCTATCATAGCAATCCATTAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCaagaa                                                                              <  1:153922/141‑1 (MQ=255)
                                                      gAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGt                                                                            <  1:323812/141‑1 (MQ=255)
                                                            tAACGATTTAGAAGATGTTATTAATTATGCATATCATAACAAACAAAAGACAACGTAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTaa                                                                      <  1:75605/141‑1 (MQ=255)
                                                                       aataTGTTAATAATTATGCATATCATAGCAATCCAATAACTACAGCGTTTGAAGATTTGTTATATAGGGTTGATGGTAGTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACa                                                           <  1:194120/138‑1 (MQ=255)
                                                                                             tCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTa                                     >  2:227877/1‑141 (MQ=255)
                                                                                               aTAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATc                                   <  2:224836/141‑1 (MQ=255)
                                                                                                   cAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGATGTATATTTTGATAGTCATGTTGATCAAGAAGTCCTTAATCATAGCTAAAGTCAATGGATTGAATTCACGTAGCCAac                               >  2:255105/1‑141 (MQ=255)
                                                                                                    aaTCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATGTTGTTATCCAaca                              <  2:324207/141‑1 (MQ=255)
                                                                                                       ccAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCAacagaa                           >  2:218366/1‑140 (MQ=255)
                                                                                                                   gagTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCAACAGACAGAACAGAAGtt               <  1:71640/141‑1 (MQ=255)
                                                                                                                       ttGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCAACAGACGGAACAGAAGtttatt           <  1:248497/141‑1 (MQ=255)
                                                                                                                         gAAGATTTGTTATATAGGGTAGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCAACAGACAGAACAGAAGtttattta         >  1:234594/1‑141 (MQ=255)
                                                                                                                                tGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTGATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCAACAGACAGAACAGAAGTTTATTTAAATGACt  >  1:220496/1‑141 (MQ=255)
                                                                                                                                tGTTATATAGGGTTGATGGTACTCATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCAACAGACAGAACAGAAGTTTATTTAAATGACt  >  2:111912/1‑141 (MQ=255)
                                                                                                                                         |                                                                                                                                   
AGGTTCTAAACGTCAAAAGTCTTCAGCACGTAAAAATACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATATGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCAACAGACAGAACAGAAGTTTATTTAAATGACT  >  CP000730/1002063‑1002331

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A