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
A2 F1 I1 R1 748 32.0 1685426 92.6% 1560704 103.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,786,729 G→A pseudogene (333/2253 nt) ygaQ → uncharacterized protein, putative enzyme

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,786,7290GA100.0% 133.7 / NA 42pseudogene (333/2253 nt)ygaQuncharacterized protein, putative enzyme
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (22/20);  total (22/20)

ATCTGTTAAAAAACGATTATAAAATTTCCCTTTCTCCAGATACAACTTACCGAGAGTTGAATAAAGCAGCACAGCGTAGCATTACAGCGCCAGACAGGATAGGAGAAAGAAAAACATAGGTTTATCAACGAGATACAATGATTGAAAGAGGTGATAACAGCGGTGTTTATCAGTATGGTCGTGCTGAACATTTCACCCACATTATATCTGACAAACCTTCCCCAAAAGATAAATATGTTGCATATGCTATTAA  >  NC_000913/2786611‑2786863
                                                                                                                      |                                                                                                                                      
aTCTGTTAAAAAACGATTATAAAATTTCCCTTTCTCCAGATACAACTTACCGAGAGTTGAATAAAGCAGCACAGCGTAGCATTACAGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATaaatg                                                                                                                    >  2:415386/1‑135 (MQ=255)
aTCTGTTAAAAAACGATTATAAAATTTCCCTTTCTCCAGATACAACTTACCGAGAGTTGAATAAAGCAGCACAGCGTAGCATTACAGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATaaatg                                                                                                                    >  2:124581/1‑135 (MQ=255)
 tCTGTTAAAAAACGATTATAAAATTTCCCTTTCTCCAGATACAACTTACCGAGAGTTGAATAAAGCAGCACAGCGTAGCATTACAGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATaa                                                                                                                       >  1:226825/1‑134 (MQ=255)
 tCTGTTAAAAAACGATTATAAAATTTCCCTTTCTCCAGATACAACTTACCGAGAGTTGAATAAAGCAGCACAGCGTAGCATTACAGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATaa                                                                                                                       >  1:238786/1‑134 (MQ=255)
 tCTGTTAAAAAACGATTATAAAATTTCCCTTTCTCCAGATACAACTTACCGAGAGTTGAATAAAGCAGCACAGCGTAGCATTACAGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATaa                                                                                                                       <  2:238786/135‑2 (MQ=255)
 tCTGTTAAAAAACGATTATAAAATTTCCCTTTCTCCAGATACAACTTACCGAGAGTTGAATAAAGCAGCACAGCGTAGCATTACAGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATaa                                                                                                                       <  2:226825/135‑2 (MQ=255)
     ttAAAAAACGATTATAAAATTTCCCTTTCTCCAGATACAACTTACCGAGAGTTGAATAAAGCAGCACAGCGTAGCATTACAGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGa                                                                                                              >  1:808213/1‑139 (MQ=255)
       aaaaaaCGATTATAAAATTTCCCTTTCTCCAGATACAACTTACCGAGAGTTGAATAAAGCAGCACAGCGTAGCATTACAGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGaaa                                                                                                            <  2:80249/139‑1 (MQ=255)
                      aaTTTCCCTTTCTCCAGATACAACTTACCGAGAGTTGAATAAAGCAGCACAGCGTAGCATTACAGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCg                                                                                             <  1:124581/139‑1 (MQ=255)
                         ttCCCTTTCTGCAGCTACAAATGACCGAGAGATGAATAAAGCAGCACAGCGTAGCATTACAGCGTGAGACATGATAGGAGCAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAAGAGCGgtg                                                                                          <  2:395420/139‑1 (MQ=255)
                              tttCTCCAGATACAACTTACCTAGAGTTGAATAAAGCAGCACAGCGTAGCATTACAGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCg                                                                                             <  1:567080/131‑1 (MQ=255)
                              tttCTCCAGATACAACTTACCGAGAGTTGAATAAAGCAGCACAGCGTAGCATTACAGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCg                                                                                             >  2:567080/1‑131 (MQ=255)
                              tttCTCCAGATACAACTTACCGAGAGTTGAATAAAGCAGCACAGCGTAGCATTACAGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCGGTGTTTAt                                                                                     <  2:808213/139‑1 (MQ=255)
                              tttCTCCAGATACAACTTACCGAGAGTTGAATAAAGCAGCACAGCGTAGCATTACAGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCGGTGTTTAt                                                                                     <  1:305201/139‑1 (MQ=255)
                                  tcCAGATACAACTTACCGAGAGTTGAATAAAGCAGCACAGCGTAGCATTACAGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCGGTGTTTATCAGt                                                                                 >  2:604/1‑139 (MQ=255)
                                      gATACAACTTACCGAGAGTTGAATAAAGCAGCACAGCGTAGCATTACAGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCGGTGTTTATCAGTATgg                                                                             >  1:115677/1‑139 (MQ=255)
                                            aCTTGCCGAGAGTTGAATAAAGCAGCACAGCGTAGCATTACAGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCaa                                                                                                                               <  2:508274/84‑1 (MQ=255)
                                            aCTTACCGAGAGTTGAATAAAGCAGCACAGCGTAGCATTACAGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCaa                                                                                                                               >  1:508274/1‑84 (MQ=255)
                                            aCTTACCGAGAGTTGAATAAAGCAGCACAGCGTAGCATTACAGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACg                                                                                                                             <  2:392979/86‑1 (MQ=255)
                                            aCTTACCGAGAGTTGAATAAAGCAGCACAGCGTAGCATTACAGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACg                                                                                                                             >  1:392979/1‑86 (MQ=255)
                                                                     cacaGCGTAGCATTACAGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCg                                                                                             >  2:798253/1‑92 (MQ=255)
                                                                     cacaGCGTAGCATTACAGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCg                                                                                             >  2:1561/1‑92 (MQ=255)
                                                                     cacaGCGTAGCATTACAGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCg                                                                                             <  1:1561/92‑1 (MQ=255)
                                                                     cacaGCGTAGCATTACAGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCg                                                                                             <  1:798253/92‑1 (MQ=255)
                                                                                  tACAGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGCAAGAGGTGATAACAGCGGTGTTTATCAGTATGGTCGTGCTGAACATTTCACCCACATTATATCTGACAAACCTTccc                                 >  2:300120/1‑139 (MQ=255)
                                                                                      gcgcCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCGGTGTTTATCAGTATGGTCGTGCTGAACATTTCACCCACATTATATCTGACAAACCTTCCCCaaa                             >  2:434450/1‑139 (MQ=255)
                                                                                       cgcCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGAt                                                                                                                         >  1:532560/1‑47 (MQ=255)
                                                                                       cgcCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGAt                                                                                                                         <  2:532560/47‑1 (MQ=255)
                                                                                         ccAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGaaa                                                                                                            >  1:554124/1‑57 (MQ=255)
                                                                                         ccAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCGGTGTTTATCAGTATGGTCGTGCTGAACATTTCACCCACATTATATCTGACAAACCTTCCCCAAAAGa                          >  1:351424/1‑139 (MQ=255)
                                                                                         acAGACAGGATAGGAGATAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGaaa                                                                                                            <  2:554124/56‑1 (MQ=255)
                                                                                                ggATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCGGTGTTTATCAGTATGGTCGTGCTGAACATTTCACCCACATTATATCTGACAAACCTTCCCCAAAAGATAAatat                   <  1:434450/139‑1 (MQ=255)
                                                                                                           agaaaAACATAAGTTTATCAACGAGATA‑AATGATTGaaa                                                                                                            <  2:407236/39‑1 (MQ=37)
                                                                                                           agaaaAACATAAGTTTATCAACGAGATA‑AATGATTGaaa                                                                                                            >  1:407236/1‑39 (MQ=37)
                                                                                                           agaaaAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAg                                                                                               <  2:495060/52‑1 (MQ=255)
                                                                                                           agaaaAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAg                                                                                               >  1:495060/1‑52 (MQ=255)
                                                                                                           agaaaAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCGgt                                                                                           <  2:138916/56‑1 (MQ=255)
                                                                                                           agaaaAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCGgt                                                                                           >  1:138916/1‑56 (MQ=255)
                                                                                                           agaaaAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCGGTGTTTATCAGTATGGTCGTGCTGAACATTTCACCCACATTATATCTGACAAACCTTCCCCAAAAGAt                         <  1:77097/122‑1 (MQ=255)
                                                                                                           agaaaAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCGGTGTTTATCAGTATGGTCGTGCTGAACATTTCACCCACATTATATCTGACAAACCTTCCCCAAAAGAt                         >  2:77097/1‑122 (MQ=255)
                                                                                                           agaaaAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCGGTGTTTATCAGTATGGTCGTGCTGAACATTTCACCCACATTATATCTGACAAACCTTCCCCAAAAGATAAATATGTTGCATATGc        >  2:220141/1‑139 (MQ=255)
                                                                                                                 aCATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCGGTGTTTATCAGTATGGTCGTGCTGAACATTTCACCCACATTATATCTGACAAACCTTCCCCAAAAGATAAATATGTTGCATATGCTATTaa  <  1:415386/139‑1 (MQ=255)
                                                                                                                      |                                                                                                                                      
ATCTGTTAAAAAACGATTATAAAATTTCCCTTTCTCCAGATACAACTTACCGAGAGTTGAATAAAGCAGCACAGCGTAGCATTACAGCGCCAGACAGGATAGGAGAAAGAAAAACATAGGTTTATCAACGAGATACAATGATTGAAAGAGGTGATAACAGCGGTGTTTATCAGTATGGTCGTGCTGAACATTTCACCCACATTATATCTGACAAACCTTCCCCAAAAGATAAATATGTTGCATATGCTATTAA  >  NC_000913/2786611‑2786863

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A