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
A5 F58 I0 R1 46 56.2 1222162 96.0% 1173275 141.0

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% 112.2 / ‑6.5 39I216N (ATT→AAT) oppD_4Oligopeptide transport ATP‑binding protein OppD
Reads supporting (aligned to +/- strand):  ref base A (0/0);  major base T (16/22);  minor base C (0/1);  total (16/23)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

ACTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAAATGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTG  >  USA300TCH1516_ALE/1416326‑1416590
                                                                                                                                    |                                                                                                                                    
aCTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAAGGATTTGACCTTCTTTTAAAACATAATTGTACTGa                                                                                                                              >  1:107425/1‑141 (MQ=255)
           gTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTATTATTACATGATGCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCaa                                                                                                                   >  1:571111/1‑141 (MQ=255)
              aTCCATCTTTAGTTGTGTTCGATATTTAATTAGACGTTCATTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTGTAAAACATAATTGTACTTCCAATATTTCAATAc                                                                                                                <  2:152056/141‑1 (MQ=255)
                         aTTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGt                                                                                                     <  1:459209/141‑1 (MQ=255)
                             tgtTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTAtg                                                                                                 <  2:83341/141‑1 (MQ=255)
                             tgtTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTAtg                                                                                                 <  2:236724/141‑1 (MQ=255)
                               ttCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCCTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTAtgtg                                                                                               >  1:512134/1‑141 (MQ=255)
                                    tatTTCATTGGGCGTTCAGTATACGGATGCATATGTTCATACTTGAAATGATTAATTTTACCTCGTTCAATGATTTTACCTTCTTTTAAAACATAATTGTATTGACAATATTTCAATACATGACTTAAGTTATGTGTGata                                                                                          <  2:118618/141‑1 (MQ=255)
                                      tttAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGataaa                                                                                        >  2:370763/1‑140 (MQ=255)
                                                cGTTCAGTATACGGATGCAAATGCTCAGACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGtt                                                                              <  1:594414/141‑1 (MQ=255)
                                                    cAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGGTTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATATTAAATAATGTTTGAc                                                                          >  1:191046/1‑141 (MQ=255)
                                                    cAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGATATGTGGGATAAGAAATAATGTTTAAc                                                                          >  2:594024/1‑141 (MQ=255)
                                                      gTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCa                                                                        >  1:60822/1‑141 (MQ=255)
                                                        agaccgATGCACACGCTCATACCTGACATGATTAATTTTACCTCGTTCAATGATTTGCCCTTCTTTTAAAACATAATTGTACTGACAATACTTCCATACATCACTTTATTTCTTTGTGATAATAAATTCTGTTCGACCTTg                                                                      <  2:467511/136‑1 (MQ=255)
                                                              aTGCAAATGCTCATACTTGAACTGAGCGATAGTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTaa                                                                >  2:130971/1‑141 (MQ=255)
                                                                    aTGCGCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAat                                                          <  2:515914/141‑1 (MQ=255)
                                                                     agCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAata                                                         <  2:564497/140‑1 (MQ=255)
                                                                      gCTCATACTTGAAATGATTAATATTACCTCGTTCAATGAGTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAatat                                                        >  2:336936/1‑141 (MQ=255)
                                                                        tCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGc                                                      <  1:434664/141‑1 (MQ=255)
                                                                          atccTTCAAATGATTAATATTACCTGGTTCAATGATTTGACCTCCTTTGACAACATAACTTTACTGACAATATTTCAATACATGTCTTAAGTTATGTGTGATAATAAATAATGTTTGACCCTGTTCTAATCCCATATGCTg                                                    <  2:28100/138‑1 (MQ=255)
                                                                          aTACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTg                                                    <  2:577753/141‑1 (MQ=255)
                                                                                 aaaTGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGGCTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGtaacatt                                             >  2:150040/1‑137 (MQ=255)
                                                                                       ttAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGATAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAACATGCTGTAATAAATCCATc                                       <  1:342305/141‑1 (MQ=255)
                                                                                       ttAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATcccac                                       >  2:60596/1‑138 (MQ=255)
                                                                                       ttAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGGGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATc                                       >  1:309083/1‑141 (MQ=255)
                                                                                       atAATATTACCTCGTTCAATGACTTGACCTTCTTTTAAAAAATAATTGTGCTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATACTGTTTGACCATGTTCTAGTACAATATGCTGTAATAAATCCTTc                                       >  2:243151/2‑141 (MQ=255)
                                                                                        tAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATtcatca                                      >  2:125184/1‑141 (MQ=255)
                                                                                          atatTACCTCGTTCAATGATTTGACCTTTTTTTAAAACACAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACt                                    <  1:302754/141‑1 (MQ=255)
                                                                                          atatTACCTCGTTCAATGACTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAGATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAACCCATCACt                                    <  2:450619/141‑1 (MQ=255)
                                                                                              tACCTCGTTCAATGCTTTGACCTTCTTTTAAAACATAATTGGACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGAt                                <  1:14424/141‑1 (MQ=255)
                                                                                              tACCTCGTACAATGCTTTGACCTTCTTTTAAAACATAATTGGACTGACAATATTCCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGAt                                <  1:230946/141‑1 (MQ=255)
                                                                                                ccTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTa                              <  2:496269/141‑1 (MQ=255)
                                                                                                     ttaaaTGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGtt                         <  2:220363/138‑1 (MQ=255)
                                                                                                        aaTGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCaa                      >  1:349031/1‑141 (MQ=255)
                                                                                                        aaTGATTTGACCGTCTTTTAANANATANTTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATCTTTGACCATGGTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCaa                      <  1:368268/141‑1 (MQ=255)
                                                                                                               tGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATcc               >  1:217126/1‑141 (MQ=255)
                                                                                                                      cttTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAatgatg        <  2:60822/141‑1 (MQ=255)
                                                                                                                       tttaAAAACATAATTTTACTGAAAATATTTTAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGc       <  2:191046/141‑1 (MQ=255)
                                                                                                                            aaaCATAATTGTACTGACAATACTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTg  <  1:446250/141‑1 (MQ=255)
                                                                                                                                    |                                                                                                                                    
ACTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAAATGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTG  >  USA300TCH1516_ALE/1416326‑1416590

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