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 F178 I0 R1	41	49.4	1100758	95.6%	1052324	140.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	629,681	C→A	100%	L84I (CTA→ATA)	USA300HOU_RS02990 →	3‑hexulose‑6‑phosphate synthase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	629,681	0	C	A	100.0%	135.2 / NA	44	L84I (CTA→ATA)	USA300HOU_RS02990	3‑hexulose‑6‑phosphate synthase
Reads supporting (aligned to +/- strand): ref base C (0/0); new base A (24/20); total (24/20)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GAAGGTTTACCAGCAGTTAAACATATGGCAGACAACATTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATACTAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGATTTAGAAAAACGTGCAAAAGAACTAGATGAAATGG  >  USA300TCH1516_ALE/629546‑629810

gAAGGTTTACCAGCAGTTAAACATATGGCAGACAACATTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAgg                                                                                                                               <  1:49243/140‑1 (MQ=255)

     tttACCAGCAGTTAAACATATGGCAGACAACATTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGgtgtgg                                                                                                                          >  1:217311/1‑138 (MQ=255)

     tttACCAGCAGTTAAACATATGGCAGACAACATTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTg                                                                                                                          <  1:445544/140‑1 (MQ=255)

     tttACCAGCAGTTAAACATATGGCAGACAACATTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTg                                                                                                                          >  1:521613/1‑140 (MQ=255)

     tttACCAGCAGTTAAACATATGGCAGACAACATTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGAAGTAATTACAATAATAGATGTTg                                                                                                                          >  1:217328/1‑140 (MQ=255)

     tttACCAGCAGTTAAACATATGGCAGACAACATTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCAAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTg                                                                                                                          >  1:430547/1‑140 (MQ=255)

         ccAGCAGTTAAACATATGGCAGACAACATTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGAATAAGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCaga                                                                                                                      >  1:115529/1‑140 (MQ=255)

                ttAAACATATGGCAGACAACATTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCa                                                                                                               <  1:292213/140‑1 (MQ=255)

                   aaCATATGGCAGACAACATTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAAAATGACGCGGATGTAATTACAATAAGAGTGTTTGCAGAAAATGCATCa                                                                                                            >  1:125081/1‑140 (MQ=255)

                      atatGGCAGACAACATTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGGTTATGGAGTTTGCCAAGCAACTAAATCTGTCGCGGATGTAATTACAATAATAGGTGTTGCAGAATATGCATCCAtt                                                                                                         >  2:59949/1‑140 (MQ=255)

                        atGGCAGACAACATTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTaa                                                                                                       <  2:348157/140‑1 (MQ=255)

                          ggCAGACAACATTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAag                                                                                                     <  1:254475/140‑1 (MQ=255)

                                   caTTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGACCATGCATCAATTAAAGCAGCTATTg                                                                                            >  2:411725/1‑140 (MQ=255)

                                   caTTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTg                                                                                            >  2:520823/1‑140 (MQ=255)

                                    aTTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTga                                                                                           <  1:363754/140‑1 (MQ=255)

                                    aTTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTga                                                                                           <  1:369205/140‑1 (MQ=255)

                                     ttAGTAATGGAAGAGTAATAGGAGACAAGAATATGATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGACGTAATTACAATAATAGGTGTTGCAGAAGGTGAATAAATGAAAGAACCTATTgaa                                                                                          >  2:460157/1‑140 (MQ=255)

                                          aaTGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGc                                                                                     <  1:475607/140‑1 (MQ=255)

                                          aaTGTAAAAGTAGTAGTAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGc                                                                                     <  1:110883/140‑1 (MQ=255)

                                          aaTATAAAACTATTAGCAGACATGAAAATTATAGCTGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATTTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTgaagaatc                                                                                     <  2:454404/140‑3 (MQ=255)

                                                  aGTATTAGCAGACATGAAAATTATGGATGCAGCTGATTATGAAGTTAGACAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATaaaa                                                                             <  1:207679/140‑1 (MQ=255)

                                                  aGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAAGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATaaaa                                                                             <  1:427357/140‑1 (MQ=255)

                                                    tATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGATCATAAAaat                                                                           >  2:396022/1‑140 (MQ=255)

                                                     aTTAGCAGACATGAAAATTATAGATGCAACTGATTATGAAATTAGCAAAGCACATAAATTTGGAGAGGGTGTAATTAAAATAATAGGTGTTGCAGAGGATGCATCAATTAAAGCACCTATTGAAGAAGCTCATAGAaata                                                                          >  2:143306/1‑140 (MQ=255)

                                                        aGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTAGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCGCATAAAAataata                                                                       >  1:141200/1‑140 (MQ=255)

                                                         gCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAAAAGCTCAtaaaaataaaaa                                                                      >  2:521657/1‑140 (MQ=255)

                                                              cATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGCAGCCCATAAAAATAATAAACAAt                                                                 >  2:549911/1‑140 (MQ=255)

                                                                tGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTa                                                               <  2:51433/140‑1 (MQ=255)

                                                                agAAAATTACAGACGCAGCTTATTATGAAATTAGCCAGGCAATTAAACTTGGCCTGGATGTAATTACAATAATAGGTCTTGCAGAAGATGCATCAATTAAAGCAGCTATTGTAGAAGCTCATAAAAATAATAAACAATTa                                                               <  2:984/139‑1 (MQ=255)

                                                                 gAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAAtatc                                                              >  2:270928/1‑137 (MQ=255)

                                                                      ttATAGATGCAGCTGATTATTAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGtt                                                         <  2:321125/140‑1 (MQ=255)

                                                                          aGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGata                                                     >  2:414612/1‑140 (MQ=255)

                                                                           gATGCAGCTGATTATGTAGTTGGCCAAGCAGTTAAATTTGGCACGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGGAGCTCATAAAAATAATAAACAATTACTAGTTGatat                                                    >  1:273109/1‑140 (MQ=255)

                                                                                        aTGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACAAGTTGATATGATTGCTGTTGaa                                       >  2:113217/1‑140 (MQ=255)

                                                                                           aaGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGAt                                    >  1:105893/1‑140 (MQ=255)

                                                                                                       cAATTAAATTTGGCGTGGATGTAATTACTATAATAGGTGTTGCAGAAGATGTATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGATTTAGAAAAACGt                        <  1:35948/140‑1 (MQ=255)

                                                                                                         aTTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGATTTAGAAAAACGTGc                      <  1:311241/140‑1 (MQ=255)

                                                                                                            aaaTTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCGTCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGATCCAGAAAAACGTGCaaa                   >  2:355907/1‑140 (MQ=255)

                                                                                                              aTTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGATTTAGAAAAACGTGCAAAAg                 <  2:147081/140‑1 (MQ=255)

                                                                                                                   gcgcGGATGTAATTACAATAATAGGTGTTGCAGACGATGCAGCAATTAAAGCAGCGATCGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTAATATGATTACTAATCAAGATTTAGAAAAACGTGAGAAAGAAcga            >  1:77589/1‑138 (MQ=255)

                                                                                                                    cgcgGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGATTTAGAAAAACGTGCAAAAGAACTAg           >  2:512840/1‑140 (MQ=255)

                                                                                                                           gTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGATTTAGAAAAACGTGCAAAAGAACTAGATGAAAt    <  2:197945/140‑1 (MQ=255)

                                                                                                                            tAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGATTTAGAAAAACGTGCAAAAGAACTAGATGAAATg   >  1:472212/1‑140 (MQ=255)

                                                                                                                             aaTTACAATAACAGGTGTTTCAGAAAATGCATCAATTAAAGAAGCTATTGAAGAAGCTCATAAAAATAAGAAAAGATTACTAGTTGATATGTGTGCTGTTCAAGATTTAGAAAAACGTGCAAAAGAACTAGATGAAATgg  <  1:417782/140‑1 (MQ=255)

GAAGGTTTACCAGCAGTTAAACATATGGCAGACAACATTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATACTAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGATTTAGAAAAACGTGCAAAAGAACTAGATGAAATGG  >  USA300TCH1516_ALE/629546‑629810

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