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
A1 F169 I0 R1	75	34.0	794130	95.7%	759982	140.9

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%	81.8 / ‑6.5	27	L84I (CTA→ATA)	USA300HOU_RS02990	3‑hexulose‑6‑phosphate synthase
Reads supporting (aligned to +/- strand): ref base C (1/0); new base A (16/10); total (17/10)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

ACGAAGGTTTACCAGCAGTTAAACATATGGCAGACAACATTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATACTAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGATTTAGAAAAACGTGCAAAAGAACTAGATGAAATGGGTGCTGAT  >  USA300TCH1516_ALE/629544‑629818

aCGAAGGTTTACCAGCAGTTAAACATATGGCAGACAACATTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAg                                                                                                                                        <  1:276579/141‑1 (MQ=255)

             agcagTTAAACATATGGCAGACAACATTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCagaaga                                                                                                                           <  2:51090/141‑1 (MQ=255)

                agTTAAACATATGGCAGACAACATTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGc                                                                                                                        >  2:321043/1‑141 (MQ=255)

                     aaCATATGGCAGACAACATTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCaa                                                                                                                   >  1:318205/1‑141 (MQ=255)

                     aaCATATGGCAGACAACAATAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATAATGAAGTTAGCCAAGGAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCaa                                                                                                                   <  1:296929/141‑1 (MQ=255)

                      aCATATGGAAGACAACATTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAAt                                                                                                                  <  1:199622/141‑1 (MQ=255)

                                    acaTTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTg                                                                                                    >  2:299284/1‑141 (MQ=255)

                                           tAATGTAAAAGTAGTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGc                                                                                             <  1:183425/141‑1 (MQ=255)

                                             aTGTAAAAGAATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTc                                                                                           <  1:138968/141‑1 (MQ=255)

                                                   aaGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGGGCGGATGTAATTACAATCATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTCAAGAAGCTCATaaaa                                                                                     >  1:79197/1‑141 (MQ=255)

                                                     gTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAaat                                                                                   <  1:155910/141‑1 (MQ=255)

                                                      tATTAGCAGACATGAAAATTATAGATACATGTGATACAGCAGTTAGACAATCAACTAAAGTCGGAAAGGATAAAATTACGACACTAGGAGGTGCGGAAGATGCATGAATTAAAGCAGCAATTGCAGAAGAGAATAAAaata                                                                                  >  2:163117/1‑141 (MQ=255)

                                                                       aTTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGATGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGtt                                                                 >  2:283867/1‑141 (MQ=255)

                                                                       aTTATAGATGCAGCAGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATCGAAGAAGCTCATAAAAATAATAAACAATTACTAgat                                                                 >  1:218950/1‑139 (MQ=255)

                                                                        ttATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGATGATGCATTAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTg                                                                <  2:63593/141‑1 (MQ=255)

                                                                                      gagtATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAACCAATTACTAGTGGATATGATTGATGtt                                                  >  2:103819/4‑141 (MQ=255)

                                                                                      gATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCGTAAAAATAATAAACAATTAATAGTTGATATGATTACTGtt                                                  >  1:66573/1‑141 (MQ=255)

                                                                                      gATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGtt                                                  >  1:261417/1‑141 (MQ=255)

                                                                                       aTTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTACTTGATATGATTGCTGttt                                                 >  2:346360/1‑140 (MQ=255)

                                                                                           tGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGa                                             >  1:63010/1‑141 (MQ=255)

                                                                                                   gCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGATTTAGaaa                                     >  2:361002/1‑141 (MQ=255)

                                                                                                       aGCAATTAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGATTTAGAAAAACg                                 <  1:284934/141‑1 (MQ=255)

                                                                                                             tAAATTTGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGATTTAGAAAAACGTGCaaa                           >  2:389616/1‑141 (MQ=255)

                                                                                                             tAAATTTAGCGCGGAGGTAATTACAATAATATGTGTTGCAGAAAATGCATCAATTAAAACAGCTATGGAAGAAGCTCATAAAAATAATAAACAATAAATAGTTGATATAATTGCAGTTCAAGATCTAGACAAACGTGCaaa                           >  2:322860/1‑141 (MQ=255)

                                                                                                                  ttGGCGCGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGATTTAGAAAAACGTGCAAAAGAAc                      >  1:141993/1‑141 (MQ=255)

                                                                                                                     gcgcGGATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGATTTAGAAAAACGTGCAAAAGAACTAg                   >  1:56919/1‑141 (MQ=255)

                                                                                                                         ggATGTAATTACAATAATAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGATTTAGAAAAACGTGCAAAAGAACTAGATGa               <  1:145700/141‑1 (MQ=255)

                                                                                                                                      ataataGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGATTTAGAAAAACGTGCAAAAGAACTAGATGAAATGGGTGCTGAt  <  1:156359/141‑1 (MQ=255)

ACGAAGGTTTACCAGCAGTTAAACATATGGCAGACAACATTAGTAATGTAAAAGTATTAGCAGACATGAAAATTATAGATGCAGCTGATTATGAAGTTAGCCAAGCAATTAAATTTGGCGCGGATGTAATTACAATACTAGGTGTTGCAGAAGATGCATCAATTAAAGCAGCTATTGAAGAAGCTCATAAAAATAATAAACAATTACTAGTTGATATGATTGCTGTTCAAGATTTAGAAAAACGTGCAAAAGAACTAGATGAAATGGGTGCTGAT  >  USA300TCH1516_ALE/629544‑629818

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