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 F169 I0 R1 75 34.0 794130 95.7% 759982 140.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 1,416,458 A→T 100% I216N (ATT→AAT)  oppD_4 ← Oligopeptide transport ATP‑binding protein OppD

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,416,4580AT100.0% 104.2 / NA 33I216N (ATT→AAT) oppD_4Oligopeptide transport ATP‑binding protein OppD
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (18/15);  total (18/15)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

ACTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAAATGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACT  >  USA300TCH1516_ALE/1416326‑1416589
                                                                                                                                    |                                                                                                                                   
aCTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATATTACTGa                                                                                                                             >  2:128648/1‑141 (MQ=255)
   cAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCCATGATTTGACCTTCTTTTAAAACATAATTGAACTGACaa                                                                                                                          >  2:343967/1‑141 (MQ=255)
           gTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCaa                                                                                                                  >  1:55063/1‑141 (MQ=255)
                      ttAATGGTGTACTATATTTAATTAGACGTGGTGTATACGGAAGCAAAGGCTCATAATTGAAATGATTAATACTACCTCGTTAAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTa                                                                                                       <  1:594/141‑1 (MQ=255)
                       tAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCACTACATGACTTaa                                                                                                      >  1:317487/1‑141 (MQ=255)
                          ttGTGTTCTATATTTAATTAGTCGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGtt                                                                                                   <  2:225607/141‑1 (MQ=255)
                          ttGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGCTTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGGCGTTACAACACTCCATGACTAAAGtt                                                                                                   >  2:276146/1‑141 (MQ=255)
                           tgtgTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTa                                                                                                  <  2:191203/141‑1 (MQ=255)
                                     atTTAATTAGACGTTCAGTATACGGATGCAAATGATCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGataa                                                                                        >  1:233056/1‑141 (MQ=255)
                                      tttAATTCGACGTGCAGTATACGGATGCAAATGCTCATACTTGAAATGATTACTATTGCCTCCTACAATGATTTGACCTTCTGTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGataat                                                                                       <  2:69150/141‑1 (MQ=255)
                                      tttAATTAGGCGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGataat                                                                                       <  2:195058/141‑1 (MQ=255)
                                             aGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAataaataaa                                                                                >  1:43571/1‑140 (MQ=255)
                                             aGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAaataat                                                                                >  1:347359/1‑141 (MQ=255)
                                             aGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAaataat                                                                                >  2:329267/1‑141 (MQ=255)
                                                  ttCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCCATACATGACTTAAGTTATTAGTGATAATAAATAATTTTTg                                                                           >  1:345516/1‑141 (MQ=255)
                                                  tgcAGTATACGGATGCATATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTg                                                                           <  2:214182/139‑1 (MQ=255)
                                                          acagaggCAAAGGCTCATACTTGAAATGATGAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGtt                                                                   >  2:231637/7‑141 (MQ=255)
                                                          aCGGATGGAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATCTTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGtt                                                                   <  2:242126/141‑1 (MQ=255)
                                                          aCGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAAAATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGtt                                                                   >  2:134004/1‑141 (MQ=255)
                                                              aTGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTaa                                                               <  1:353149/141‑1 (MQ=255)
                                                                           tACGTGAAATGATTAATATTACCTCGGTCAAGGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGt                                                  <  2:345516/141‑1 (MQ=255)
                                                                                gAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGtaataa                                             >  2:302903/1‑141 (MQ=255)
                                                                                                cccgtttCAATGATTTGACCTTCTTTTAAAACAGAATTTTACTGACAATACTTCAATACATGACTTAATTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTa                             <  1:247954/136‑1 (MQ=255)
                                                                                                 cTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTAc                            >  1:133439/1‑141 (MQ=255)
                                                                                                    gTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGt                         <  1:329267/141‑1 (MQ=255)
                                                                                                          tGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCaaac                   >  1:315608/1‑140 (MQ=255)
                                                                                                           gATTTGACCTTCTTTTAAAACATAATTGGACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGc                  <  2:108239/141‑1 (MQ=255)
                                                                                                            aTTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGCTAATAAATAATGTTTGACCATGTGCTAATACAATATGCTGTAATAAATCTATCACTTGATTACTGTTCAAAGCa                 <  1:289038/141‑1 (MQ=255)
                                                                                                             tttGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCAt                >  1:305378/1‑141 (MQ=255)
                                                                                                             tttGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCAt                >  1:67888/1‑141 (MQ=255)
                                                                                                                 aCCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCaa            <  2:55063/141‑1 (MQ=255)
                                                                                                                     tcttATAAAACATAATTGTACTGACAACATATCAGAACATGACTTAGGTTAGGTGTGATGATATAGACGGATTTGCCATTTGCTAATGCTATATGCTGTAATAAAGCCATCACTTGTTTACCGTTCAAAGCATCCAatgat        <  2:390760/141‑1 (MQ=255)
                                                                                                                           aaaaCATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTANCNTTCGATGNATCCAatgatgtacct  >  1:322359/1‑136 (MQ=255)
                                                                                                                                    |                                                                                                                                   
ACTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAAATGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACT  >  USA300TCH1516_ALE/1416326‑1416589

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