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	2,010,363	C→T	100%	C146Y (TGT→TAT)	USA300HOU_RS10125 ←	Putative multidrug export ATP‑binding/permease protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,010,363	0	C	T	100.0%	93.7 / NA	34	C146Y (TGT→TAT)	USA300HOU_RS10125	Putative multidrug export ATP‑binding/permease protein
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (19/15); total (19/15)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TTTCACGTGTCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATACAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTAAATGGTTG  >  USA300TCH1516_ALE/2010226‑2010497

tttCACGTGTCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATaa                                                                                                                                      >  2:347382/1‑140 (MQ=255)

 ttCACGTTGCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGCTAAAATGTAAAATGGGAAGATAAAAACTGACGCTGAAGTGAATTTCACATCTAAAAAGAACCTTATGGATAGTGCAATAATAATTGTTATATAAt                                                                                                                                     <  2:87891/140‑1 (MQ=255)

 ttCACGTCTCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAAt                                                                                                                                     <  2:159892/140‑1 (MQ=255)

   cACGTGTCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCt                                                                                                                                   >  1:32037/1‑140 (MQ=255)

           aaTTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATCTAATCTAACCAAat                                                                                                                           >  2:278113/1‑140 (MQ=255)

                    aaTCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTATAGTCAATTTCACATCTAAAAAGAATTGTCTGCAAAGGACAATAATAATTGTTATATAATCTAACCAAAAATTCATTaa                                                                                                                  >  1:260109/1‑140 (MQ=255)

                     aTCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTaaa                                                                                                                 >  2:324494/1‑139 (MQ=255)

                     aTCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAAc                                                                                                                 >  2:51947/1‑140 (MQ=255)

                       catCCAAAGAAAACGTACACCGTTAAAATGTTAAATGGGAAGATAAACAGTGTTGCGAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAAccc                                                                                                               <  2:537030/138‑1 (MQ=255)

                       cTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAAATAGACCGTGCTGCGCAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCTATAATACTTGTTAGATAATCTACCAAAATATACATCAAacc                                                                                                               >  1:510439/1‑140 (MQ=255)

                               gAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTaaaa                                                                                                       >  1:522800/1‑140 (MQ=255)

                                   aCGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGaa                                                                                                   >  1:274023/1‑140 (MQ=255)

                                   aCGTACACAGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAATCAAATATTCATGAAACCGGTCAAAATGaa                                                                                                   >  2:237849/1‑140 (MQ=255)

                                         acCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCttt                                                                                             <  2:391821/140‑1 (MQ=255)

                                                  atgtaaaatgTGAAGATAAACATTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATGATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTc                                                                                    <  2:467408/140‑1 (MQ=255)

                                                    gtaaaatgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCaa                                                                                  >  1:520997/1‑140 (MQ=255)

                                                      aaaatgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAAca                                                                                >  2:189043/1‑140 (MQ=255)

                                                          tgGGAAGATAAAGAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTCACCCGGTTAAAATGAAATCTTTTGTTTGGTCAAcatcat                                                                            >  1:389420/1‑140 (MQ=255)

                                                          tgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATTGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCGGGTTAAAATGAAATCTTTTTTTGGTTCAAcatcat                                                                            <  2:172580/140‑1 (MQ=255)

                                                          tgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAAcatcat                                                                            >  1:1219/1‑140 (MQ=255)

                                                             gAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGATTAAAATGAAATCTTTTGTTTGTTCAACATCATTaa                                                                         >  1:91718/1‑140 (MQ=255)

                                                                  tAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCAct                                                                    >  2:460477/1‑140 (MQ=255)

                                                                           ctgctAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATAtt                                                           <  1:415265/140‑1 (MQ=255)

                                                                                                              aTGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTGATTTGATCAACATCATTAATCACACTAGATATTACTTGACCTACTTTATTATTAGCATAAAATCACGc                        >  1:448747/1‑140 (MQ=255)

                                                                                                                 gATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCATTCTAGATATGACTTGACCTACTTGATTATTAGCATAAAATCTCGCACt                     <  1:289967/140‑1 (MQ=255)

                                                                                                                 gATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACt                     <  2:524210/140‑1 (MQ=255)

                                                                                                                           taataatTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTTTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGt           <  1:55221/140‑1 (MQ=255)

                                                                                                                            aataatTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTa          <  2:520997/140‑1 (MQ=255)

                                                                                                                             ataatTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTaa         <  1:97800/140‑1 (MQ=255)

                                                                                                                              taatTGTTATATAATCTAACCACATATTCATTAGCACGGTTAAACTGACATTTTTTGTTTGTTCAACATCATTAATAACTCTCGATATTACTTGAGCAACTTGCATTTTCGCATAAAATCTGGCAATTAATGCTTGTaaa        >  2:178266/1‑140 (MQ=255)

                                                                                                                               aatTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGAACTTAAAGCTTGTAAAt       >  1:307782/1‑140 (MQ=255)

                                                                                                                                  tGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCAGAAAATCTCGCACTTAAAGCTTGTAAATGGt    <  1:76826/140‑1 (MQ=255)

                                                                                                                                  tGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACAAGATTACTAGCATAAAATCTCGCACTTAAAGCTTGTAAATGGt    <  2:501570/140‑1 (MQ=255)

                                                                                                                                    ttATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTTAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTAAATGGTTg  <  1:209674/140‑1 (MQ=255)

TTTCACGTGTCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATACAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTAAATGGTTG  >  USA300TCH1516_ALE/2010226‑2010497

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