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
A17 F172 I0 R1 42 33.2 716278 96.8% 693357 139.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 2,679,710 G→T 100% G65V (GGC→GTC)  USA300HOU_2536 → possible secretory antigen

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007302,679,7100GT100.0% 88.2 / NA 33G65V (GGC→GTC) USA300HOU_2536possible secretory antigen
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base T (19/14);  total (19/14)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GCAGATTTCACTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTA  >  CP000730/2679574‑2679837
                                                                                                                                        |                                                                                                                               
gcagATTTCACTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCaa                                                                                                                              >  1:255649/1‑140 (MQ=255)
  agATTTCACTTATCAATCCTTTGAACTAACGCATCAATCGCATGCCGCTTTTAATTATTATAGTAAAAACCAATGTACATTGTTGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATg                                                                                                                            <  2:265993/140‑1 (MQ=255)
   gATTTCACTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGc                                                                                                                           <  1:281931/140‑1 (MQ=255)
    aTTTCACTTATCAAACCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCt                                                                                                                          <  1:55847/140‑1 (MQ=255)
    aTTTCAATTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCACGCACAAGTCGGTAAACATGTTCATAATAAGTGGGTCACTGcg                                                                                                                          >  2:156129/1‑139 (MQ=255)
                   ccGTCGAACAAACGCATCAATCGCATGCCGCAGTTACTTATTATAGTAAAAACCAATGTACATGATGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTaa                                                                                                           >  1:75749/1‑139 (MQ=255)
                          aCAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCAc                                                                                                    >  1:204758/1‑140 (MQ=255)
                            aaaCGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGt                                                                                                  <  1:101580/140‑1 (MQ=255)
                              aCGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACAAGGTTCGCATATAAACGTCGCGCACAAGTCAGTAAACCTATATCTAATAGGAGGTTCAATGCTAAAAAATGGTATTACAATGCACGTaa                                                                                                >  1:30792/1‑140 (MQ=255)
                                               cGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTg                                                                               >  1:341960/1‑140 (MQ=255)
                                                gCAGTTAATTAATATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTgg                                                                              <  1:211552/140‑1 (MQ=255)
                                                        ttattaTAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTacac                                                                      >  2:352976/1‑140 (MQ=255)
                                                           ttatAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCaa                                                                   <  1:51813/140‑1 (MQ=255)
                                                            tataGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCTCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAg                                                                  <  1:120328/140‑1 (MQ=255)
                                                               aGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAATTTGGGAAACCTGTTTCTAATAAATGGGTCAATGCTAAAAATTGGTATTACAAAGCACGTAAATCAAAATAAGCGACTAGTCGTACACCAAGaaa                                                               >  2:1661/1‑140 (MQ=255)
                                                                   aaaaCCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTGAGTAAAAGTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAAttt                                                           >  2:195846/1‑140 (MQ=255)
                                                                    gaatcAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTg                                                          <  2:30792/136‑1 (MQ=255)
                                                                    aaaCCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACAAAGAAAATTTg                                                          >  1:133219/1‑140 (MQ=255)
                                                                      atctaTGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCt                                                        <  1:91453/136‑1 (MQ=255)
                                                                          aTGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCa                                                    >  1:295126/1‑140 (MQ=255)
                                                                            gTACATGATGGGCATTTAAACGTCGCGCACAAATCGGTAAACCTGTTTATAATAGATAGGTCAATGCTCAAAATTGGTAATAACATGCACGTAAGTCAACAAAAGCGACAGGTCGTACCCCAACaaacattgatgcgctt                                                  >  2:336455/1‑127 (MQ=255)
                                                                                  ggtggGCATTTAAACGTCGCGTAAAAGTCGGTAAACCTGTTTATAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCa                                            <  2:19646/140‑1 (MQ=255)
                                                                                       gCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTACTGTCATGCAATCAACTGc                                       >  1:320304/1‑140 (MQ=255)
                                                                                          tttAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAgg                                    <  2:204758/140‑1 (MQ=255)
                                                                                                 gTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACAGAAGGAtattat                             >  1:123068/1‑140 (MQ=255)
                                                                                                      gcACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACa                        >  1:131700/1‑140 (MQ=255)
                                                                                                       cacaAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAACTCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTAAAGGATATCATGGAAAt                       >  1:190400/1‑140 (MQ=255)
                                                                                                          aaGTCGTTAAACCTGTTTCTAATAGATGGGTCGATGCTAAAAATTGTTCTTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACGTGTc                    <  1:242754/140‑1 (MQ=255)
                                                                                                                   aaCCTGTTTCTGATAGATGGGTCAATGCTCACAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACTTGTCGCAgttgtt           <  2:104255/140‑1 (MQ=255)
                                                                                                                    aCCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGATATGCCGCAGttgttg          >  1:146022/1‑140 (MQ=255)
                                                                                                                      cTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGCTATTATGGACATATCGCAATTGTTGac        >  2:225549/1‑139 (MQ=255)
                                                                                                                        gTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGAAATCAACTGCAGGATATTATGGACATGTAGCAGTTGTTGacaa      >  2:352888/1‑137 (MQ=255)
                                                                                                                            cTAATAGTGGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAATAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGta  <  2:80118/140‑1 (MQ=255)
                                                                                                                                        |                                                                                                                               
GCAGATTTCACTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTA  >  CP000730/2679574‑2679837

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A