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 I1 R1 27 57.4 1363720 95.8% 1306443 135.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA USA300TCH1516_ALE 1,646,189 G→C A155G (GCA→GGA)  ypdF ← Aminopeptidase YpdF

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,646,1890GC100.0% 97.0 / NA 32A155G (GCA→GGA) ypdFAminopeptidase YpdF
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base C (12/20);  total (12/20)

TGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTGCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTAA  >  USA300TCH1516_ALE/1646062‑1646316
                                                                                                                               |                                                                                                                               
tGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTac                                                                                                                          >  1:395650/1‑135 (MQ=255)
         aTGTGGTAATGCACCTCTATGACCAAATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCGTTTACAACAGTTaa                                                                                                                 >  1:224659/1‑135 (MQ=255)
             ggTAATGCACCTCTATGACCAGCTGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCATTTCTATTAATTCGGTCATGCCTCCTTTTACAACAGTTaaaaca                                                                                                             <  2:591356/135‑3 (MQ=255)
             ggTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATGTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCTTTTTACAACAGTTATAatg                                                                                                             >  2:588885/1‑134 (MQ=255)
             ggTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTTATGTCTCCTTTTACAACAGTTAAAata                                                                                                             <  1:353971/135‑1 (MQ=255)
             ggTAATGCACCTCTATGACCAAATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACACCAGTTAAAata                                                                                                             >  1:543646/1‑135 (MQ=255)
                aaTGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAatatat                                                                                                          <  2:112499/135‑1 (MQ=255)
                        tctATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGt                                                                                                  <  2:22037/135‑1 (MQ=255)
                                     gCTACAATCGTATCGAATAATGATACATCTGCTCCTAATTCTAGCATATTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATGCATATGTTTCATCAACAata                                                                                     >  1:163495/1‑135 (MQ=255)
                                            tCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAgctg                                                                              <  2:265902/135‑1 (MQ=255)
                                             cGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAgctgc                                                                             <  2:66566/135‑1 (MQ=255)
                                              gTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCCTATGTTTCATCAACAATATTAgctgct                                                                            >  2:24856/1‑135 (MQ=255)
                                                             ccATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTACTTCTTTTTCATACATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCa                                                             >  1:236324/1‑135 (MQ=255)
                                                             ccATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCa                                                             <  2:395650/135‑1 (MQ=255)
                                                                  tGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTc                                                        <  2:54965/135‑1 (MQ=255)
                                                                  tGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGCCATGCCTCCTTGTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTc                                                        <  2:327092/135‑1 (MQ=255)
                                                                     tCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTc                                                     <  1:87272/135‑1 (MQ=255)
                                                                     tCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTc                                                     <  2:498040/135‑1 (MQ=255)
                                                                       cTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAg                                                   >  1:586517/1‑135 (MQ=255)
                                                                         aaTTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCa                                                 >  1:51964/1‑135 (MQ=255)
                                                                            tCTAGCATTTTGCTTTCTCATAGTGCCTTTAATTCTTTTTCAGTCATGCCTCCTGTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCt                                              <  2:393114/135‑1 (MQ=255)
                                                                                              aaTATTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGTTGCTTTCTGCATTAAAGCAATTTCGTCAGCATATTTGCCGTCTCTAATTTTa                            >  2:179014/1‑135 (MQ=255)
                                                                                                 atTGCCTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCt                         <  2:198098/135‑1 (MQ=255)
                                                                                                    gCCTTTAATTCTGTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACa                      <  2:273953/135‑1 (MQ=255)
                                                                                                     ccTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAg                     >  2:618393/1‑135 (MQ=255)
                                                                                                      cTTTAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGt                    <  1:383937/135‑1 (MQ=255)
                                                                                                         tAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTAtt                 <  2:215971/135‑1 (MQ=255)
                                                                                                         tAATTCTTTTTCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTAtt                 <  1:543212/135‑1 (MQ=255)
                                                                                                                  ttCAGTCATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCt        >  1:113681/1‑135 (MQ=255)
                                                                                                                      ttcttGCCTCCTTTTACAACAGTTAAAATTTACACATATTTTTTAATAACGATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCttatt    <  2:426612/131‑1 (MQ=255)
                                                                                                                        cATGCCTCCTTTTACAACAGTTCAAATATAATCATATGTTCAATCAAGAGGAACAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTaa  <  1:263654/135‑1 (MQ=255)
                                                                                                                        cATGCCTCCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTaa  <  1:579264/135‑1 (MQ=255)
                                                                                                                               |                                                                                                                               
TGCAACACCATGTGGTAATGCACCTCTATGACCAGATGCTACAATCGTATCGAATGATGGTCCATCTGCTCCTAATTCTAGCATTTTGCTTTCTAATATTGCCTTTAATTCTTTTTCAGTCATGCCTGCTTTTACAACAGTTAAAATATATTCATATGTTTCATCAACAATATTAGCTGCTTTTTGAATTAAAGCAATTTCGTCAGCATCTTTGACGTCTCTAATTTTATCTACAGTATTAGAAATGCTTATTAA  >  USA300TCH1516_ALE/1646062‑1646316

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