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 F18 I1 R1 9 56.1 1205542 96.5% 1163348 148.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA USA300TCH1516_ALE 1,416,458 A→T 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_ALE1,416,4580AT96.7% 97.2 / NA 30I216N (ATT→AAT) oppD_4Oligopeptide transport ATP‑binding protein OppD
Reads supporting (aligned to +/- strand):  ref base A (0/0);  major base T (15/14);  minor base C (0/1);  total (15/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACATGTTTTAACTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAAATG‑TACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTGGTTCGTCTG  >  USA300TCH1516_ALE/1416316‑1416599
                                                                                                                                              |                                                                                                                                              
caatattttAACTCAATCCTAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTG‑TACt                                                                                                                                         <  1:254161/144‑1 (MQ=255)
         aaCTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTG‑TACTGACAATAtt                                                                                                                                >  1:555475/1‑149 (MQ=255)
         aaCTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGCTCCGAGCTCGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTG‑TACTGACAATAtt                                                                                                                                <  1:589678/149‑1 (MQ=255)
                 cATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTG‑TACTAACAATATTTCAATACa                                                                                                                        <  1:427482/149‑1 (MQ=255)
                   tAGTAATCCCTCTTTCATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTG‑TACTGACAATATTTCAATACATg                                                                                                                      <  1:374515/149‑1 (MQ=255)
                   aaGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGACTTGACCTTCTTTTAAAACATAATTG‑TACTGACAATATTTCAATACATg                                                                                                                      <  1:272381/148‑1 (MQ=255)
                         tCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGCTGCACATGATCATACTTGAAATGATTAATATTACATCGTTCAATGATTTGACCTCCTTTTAAAACAGAATTA‑TACTGACAATATTTCAATACATGACTTaa                                                                                                                >  2:593073/1‑149 (MQ=255)
                             tctTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTG‑TACTGACAATATTTCAATACATGACTTAAGTTa                                                                                                            >  1:83585/1‑149 (MQ=255)
                              ctTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTG‑TACTGACAATATTTCAATACATGACTTAAGTTAt                                                                                                           >  1:184663/1‑149 (MQ=255)
                              ctTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTG‑TACTGACAATATTTCAATACATGACTTAAGTTAt                                                                                                           <  2:387699/149‑1 (MQ=255)
                                 ttatttggtTCTATATTTAATTAGACGTTCATTATATGTATGCATAGTGTGATACTTGAAAGGATTAATATTCCCACGGTCCATGTTTTGATCTTCCTATAAATC‑TCACTGTTACTGTCAATCTTTCTATACATGGCGTAAGTTAtatg                                                                                                        <  2:112586/142‑1 (MQ=255)
                                                   aaTTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTG‑TACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGttt                                                                                      >  1:221395/1‑149 (MQ=255)
                                                        gACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTG‑TACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCa                                                                                 >  2:46188/1‑149 (MQ=255)
                                                            ttCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTG‑TACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGtt                                                                             <  1:377960/149‑1 (MQ=255)
                                                             tCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTG‑TACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTc                                                                            <  1:272947/149‑1 (MQ=255)
                                                                 tataCGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTG‑TACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAAt                                                                        <  2:601263/149‑1 (MQ=255)
                                                                    aCGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTG‑TACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACa                                                                     <  2:470442/149‑1 (MQ=255)
                                                                     cGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTG‑TACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACaa                                                                    >  1:262960/1‑149 (MQ=255)
                                                                            aactGCTCATAGTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTG‑TACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTg                                                             <  1:80331/146‑1 (MQ=255)
                                                                            aaaTGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTG‑TACTGACAATATTTCAATACAGGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATCAAatatcatg                                                             >  2:231570/1‑145 (MQ=255)
                                                                              aTGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTG‑TACTGACAATATTTCAGTACATTACTTAAGTTGCGTCAGTAAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGta                                                           <  1:593073/149‑1 (MQ=255)
                                                                                 cTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTG‑TACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGtaata                                                        >  1:108943/1‑149 (MQ=255)
                                                                                       cTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTG‑TACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCa                                                  >  2:308748/1‑149 (MQ=255)
                                                                                        ttGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTG‑TACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCAt                                                 >  2:254585/1‑149 (MQ=255)
                                                                                                   aaTATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTG‑TACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTAc                                      >  2:436580/1‑149 (MQ=255)
                                                                                                         aCCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTG‑TACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCa                                <  2:130705/149‑1 (MQ=255)
                                                                                                            tCGTTCAATGATTTGACCTTCTTTTAAAACATAATTG‑TACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGGTTACCGTTCAAAg                             >  1:475076/1‑149 (MQ=255)
                                                                                                                tCAATGATTTGACCTTCTTTTAAAACATAATTG‑TACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATc                         >  1:503866/1‑149 (MQ=255)
                                                                                                                   aTGATTTGACCTTCTTTTAAAACATAATTG‑TACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCaa                      >  1:64444/1‑149 (MQ=255)
                                                                                                                                       aaCATAATTG‑TACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTTATTACCGTTCAAAGCATCCAATGATGCAACTGGTGCGTCTg  <  2:184663/149‑1 (MQ=255)
                                                                                                                                              |                                                                                                                                              
ACATGTTTTAACTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAAATG‑TACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTGGTTCGTCTG  >  USA300TCH1516_ALE/1416316‑1416599

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A