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
A9 F110 I0 R1	28	36.3	769303	98.8%	760071	141.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	1,513,930	A→T	100%	L413F (TTA→TTT)	USA300HOU_RS07375 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,513,930	0	A	T	100.0%	101.3 / NA	31	L413F (TTA→TTT)	USA300HOU_RS07375	hypothetical protein
Reads supporting (aligned to +/- strand): ref base A (0/0); new base T (14/17); total (14/17)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

ATTTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTACAA  >  USA300TCH1516_ALE/1513798‑1514066

atttGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTAtt                                                                                                                                  <  1:580449/141‑1 (MQ=255)

atttGTATGTATCGCTTTATGAGTAGCCATTGGCATGGGGTTTGACTCTTGGATAAAGAGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCATCATCTATGTCACCCATAAGATGTTTTATTGTAtt                                                                                                                                  >  1:462473/1‑141 (MQ=255)

  ttGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAg                                                                                                                                >  1:649396/1‑141 (MQ=255)

   tgtatgtaTCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAgg                                                                                                                               <  1:287209/141‑1 (MQ=255)

   tgtatgtaTCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGCACGCAACCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAgg                                                                                                                               <  1:402219/141‑1 (MQ=255)

                ttattaGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCa                                                                                                                  <  1:195238/141‑1 (MQ=255)

                       tagCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTg                                                                                                           >  1:293603/1‑141 (MQ=255)

                       tagCCACTGGCATGGGCTTTCTCTCTCGGATAAAGCGTCCAAAAAACACTGCAATAAAAGTACCACATCGCGTAAAAAAACCCTTATCTATATCCCTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTg                                                                                                           <  1:636948/141‑1 (MQ=255)

                        agCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTgg                                                                                                          <  1:108296/141‑1 (MQ=255)

                          ccATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACCAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGAt                                                                                                        <  1:327827/141‑1 (MQ=255)

                               ggCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTATTGCCATTATTTGGATTATcc                                                                                                   >  1:226086/1‑140 (MQ=255)

                                    ggggTTTGTCCCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTAt                                                                                              <  1:225567/141‑1 (MQ=255)

                                             ctctTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTAtt                                                                                     <  1:145930/141‑1 (MQ=255)

                                                 tGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTtata                                                                                 >  1:360233/1‑141 (MQ=255)

                                                     tAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTg                                                                             >  1:578744/1‑141 (MQ=255)

                                                      acaGCCTACAAAAAACACTGCAATAATAGTACTACATCTCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATGAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGa                                                                            <  1:659505/139‑1 (MQ=255)

                                                         gCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTGAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATAACTTATCCTTGTATTTATAATTGAAtt                                                                         >  1:283008/1‑141 (MQ=255)

                                                              cAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAatat                                                                    <  1:634518/141‑1 (MQ=255)

                                                                 aaaaTACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAAtattat                                                                 >  1:501450/1‑141 (MQ=255)

                                                                      aCTGCAATAAAAGTAGCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATAtt                                                            >  1:384549/1‑141 (MQ=255)

                                                                         gCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTaaa                                                         >  1:210615/1‑141 (MQ=255)

                                                                                    aCCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCCTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGc                                              >  1:605613/1‑141 (MQ=255)

                                                                                       acaTCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATGATTAATCCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTaa                                           <  1:556203/141‑1 (MQ=255)

                                                                                              gTAAAAAAACCAGCATCTATATCACTCAAAATATGTTTTATTGTATTAGGATTAGTAATGCCATTATTTGGATTATCACGTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACaataa                                    >  1:493248/1‑141 (MQ=255)

                                                                                                    aaaCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACt                              <  1:188456/141‑1 (MQ=255)

                                                                                                    aaaCCAGCACCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACt                              <  1:356291/141‑1 (MQ=255)

                                                                                                       ccAGCTTCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATAGTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTaa                           <  1:522537/141‑1 (MQ=255)

                                                                                                       ccAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTGATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTaa                           >  1:147569/1‑141 (MQ=255)

                                                                                                       ccAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTACACAATAATGCACTTaa                           <  1:424183/141‑1 (MQ=255)

                                                                                                                              ttGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTAc    <  1:448525/140‑1 (MQ=255)

                                                                                                                                gTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTACaa  >  1:672873/1‑141 (MQ=255)

ATTTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTACAA  >  USA300TCH1516_ALE/1513798‑1514066

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A