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 F43 I0 R1	32	68.2	1528488	95.6%	1461234	139.9

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%	120.8 / NA	38	L413F (TTA→TTT)	USA300HOU_RS07375	hypothetical protein
Reads supporting (aligned to +/- strand): ref base A (0/0); new base T (21/17); total (21/17)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TTATTTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTACA  >  USA300TCH1516_ALE/1513796‑1514065

ttatttGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATCCTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTga                                                                                                                                    >  2:633412/1‑139 (MQ=255)

   tttGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTAtt                                                                                                                                 >  1:114732/1‑140 (MQ=255)

     tgtatgtaTCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAAACCAGCATCTATATCACTCATACTATGTTTTATCGTAtca                                                                                                                                >  1:142712/1‑138 (MQ=255)

               gCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAAt                                                                                                                     >  2:604413/1‑140 (MQ=255)

                cTTTATTATAAGCCATTGGCATGGGGTTTGCCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATg                                                                                                                    <  1:223460/140‑1 (MQ=255)

                cTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATg                                                                                                                    <  1:636338/140‑1 (MQ=255)

                    attaGTAGCCATTGGCATGGTGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCat                                                                                                                <  1:446358/140‑1 (MQ=255)

                    attaGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCat                                                                                                                <  1:446586/140‑1 (MQ=255)

                       agtagCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCattat                                                                                                             <  1:124101/140‑1 (MQ=255)

                          agCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTg                                                                                                          >  1:110476/1‑140 (MQ=255)

                            ccATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATTACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGa                                                                                                        <  2:382348/140‑1 (MQ=255)

                               ttGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTa                                                                                                     >  1:495182/1‑140 (MQ=255)

                                tGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTAt                                                                                                    >  1:613198/1‑140 (MQ=255)

                                 ggCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATc                                                                                                   >  1:45471/1‑140 (MQ=255)

                                      ggggTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTa                                                                                              >  1:578801/1‑140 (MQ=255)

                                             gTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGt                                                                                       >  1:410727/1‑140 (MQ=255)

                                                  ttGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTta                                                                                  >  2:204255/1‑140 (MQ=255)

                                                     gATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTAATAGGATTATTAATGCCATTATTTGGATTATCACTTATGCTTGTATTtatag                                                                               >  1:375912/1‑139 (MQ=255)

                                                     gATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCAGAATATGTTTTATTGTATTAGGATTATTAATGCCATTCTTTGGATTATCTCTTCTCCTTGTATTTATaa                                                                               >  1:386135/1‑140 (MQ=255)

                                                      aTAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTATATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAAt                                                                              <  1:533544/140‑1 (MQ=255)

                                                       tAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAACAACCAGCTTCTAGATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAAtt                                                                             <  1:143156/140‑1 (MQ=255)

                                                       tAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAAtt                                                                             <  1:536998/140‑1 (MQ=255)

                                                        aaaGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATC‑‑TATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGaa                                                                          <  2:623297/140‑1 (MQ=255)

                                                         aaGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGa                                                                           >  2:238539/1‑140 (MQ=255)

                                                                   aaaaTACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTCATGGCTAAATGGGGATTATCACTTATCCTTGTATTTATAATTGAATTAAtatta                                                                 >  2:339653/1‑140 (MQ=255)

                                                                   aaaaTACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTCTTTATAATTGAATTAAtatta                                                                 >  1:648640/1‑140 (MQ=255)

                                                                    aaaTACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACACATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAAtattat                                                                >  1:176957/1‑140 (MQ=255)

                                                                          tGCAACAAAAGTACCACATCGCGT‑AAAAAGACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTACTGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTa                                                          <  1:290005/140‑1 (MQ=255)

                                                                           acAATAAAAGTATCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTaa                                                         <  2:723307/139‑1 (MQ=255)

                                                                                   aGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATCATTGAATTAATATTATATATTAAAGAtcgtc                                                 >  1:155381/1‑140 (MQ=255)

                                                                                   aGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAGGAtcgtc                                                 >  2:292849/1‑140 (MQ=255)

                                                                                          caTCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGCTTTATTGTATTAGGATTATTAATGCCTTTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTaa                                          <  1:390663/140‑1 (MQ=255)

                                                                                                          ccAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTa                           <  1:319183/140‑1 (MQ=255)

                                                                                                               aTCTATATCACTCATAATATGTTTTATTGTACTAAGATGATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGtt                      <  1:516327/140‑1 (MQ=255)

                                                                                                                    tatCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCATTTAAAGTTTTGaa                 >  2:372319/1‑140 (MQ=255)

                                                                                                                         cTCATTATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGAc            <  1:392628/140‑1 (MQ=255)

                                                                                                                           cATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGa          <  2:110476/140‑1 (MQ=255)

                                                                                                                                   gTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTata  >  1:502700/1‑138 (MQ=255)

TTATTTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTACA  >  USA300TCH1516_ALE/1513796‑1514065

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