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 F58 I0 R1	35	61.1	1410250	95.0%	1339737	139.9

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%	141.6 / NA	44	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 (28/16); total (28/16)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TTTCACGTGTCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCA‑ATAATAATTGTTATACAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTAAATGGTTG  >  USA300TCH1516_ALE/2010226‑2010497

tttCACGTGTCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCA‑ATAATAATTGTTATATaa                                                                                                                                      >  1:385507/1‑140 (MQ=255)

               ttCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCA‑ATAATAATTGTTATATAATCTAACCAAATAtta                                                                                                                       >  1:81713/1‑139 (MQ=255)

               ttCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCA‑ATAATAATTGTTATATAATCTAACCAAATATTc                                                                                                                       >  1:274874/1‑140 (MQ=255)

                          ccAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGAACATCAT‑ATTTTTATATAATCTAACCAAATATTCATTAACCCGGt                                                                                                            >  2:496362/1‑140 (MQ=255)

                           cAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCA‑ATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGtt                                                                                                           >  2:8870/1‑140 (MQ=255)

                           cAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCA‑ATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGtt                                                                                                           >  2:224120/1‑140 (MQ=255)

                           cAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCA‑ATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGtt                                                                                                           >  2:100474/1‑140 (MQ=255)

                           cAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCA‑ATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGtt                                                                                                           >  1:596182/1‑140 (MQ=255)

                             aaGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCA‑ATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTaa                                                                                                         >  1:623702/1‑140 (MQ=255)

                                 aaaCGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCA‑ATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATg                                                                                                     >  1:269972/1‑140 (MQ=255)

                                 aaaCGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCA‑ATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATg                                                                                                     >  2:394462/1‑140 (MQ=255)

                                       acacCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCA‑ATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCt                                                                                               <  1:692613/140‑1 (MQ=255)

                                        cacCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCA‑ATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCtt                                                                                              <  1:8870/140‑1 (MQ=255)

                                             ttAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCA‑ATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTtttgtt                                                                                         <  2:596387/140‑1 (MQ=255)

                                                 aatgtaaaatgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCA‑ATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTtgtttgtt                                                                                     >  2:225049/1‑140 (MQ=255)

                                                 aaagtaaaaagGGAAAAGAAAGAACGCTGCTAAAGTAAAAAAAAAAAAAAAAAAGAACATTATGGATAGTGCA‑ATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTtgtttgtt                                                                                     <  2:484266/137‑1 (MQ=255)

                                                    gtaaaatgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACGTTATGGCTATTGCA‑ATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTGGTTCaa                                                                                  >  1:99375/1‑140 (MQ=255)

                                                            ggAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCA‑ATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTa                                                                          <  1:507884/140‑1 (MQ=255)

                                                                 aTAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCA‑ATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCAc                                                                     <  1:540163/140‑1 (MQ=255)

                                                                    aaCAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCA‑ATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCActct                                                                  <  1:624543/140‑1 (MQ=255)

                                                                      cAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCA‑ATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATGATTAATCACTCTAg                                                                >  1:336883/1‑140 (MQ=255)

                                                                              ctAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCA‑ATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACt                                                        >  1:87794/1‑140 (MQ=255)

                                                                                      aaTTTCACATCTAAAAAGAACATTATGGATAGTGCA‑ATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTAc                                                <  1:551658/140‑1 (MQ=255)

                                                                                       aTTTCACATCTAAGAAGAACATTATGGATAGTGCA‑ATGATAATTGTTATATAATCTAACAAAATATTCATTAGGCTGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAGTCACTCTAGATATTACTTGACCTACt                                               >  2:544659/1‑140 (MQ=255)

                                                                                       aTTTCACATCTAAGAAGAACATTATGGATAGTGCA‑ATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACt                                               >  1:79909/1‑140 (MQ=255)

                                                                                         ttCACATCTAAAAAGAACATTATGGATAGTGCA‑ATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTg                                             >  2:272807/1‑140 (MQ=255)

                                                                                         ttCAAATCTAAAAAGAACATTATGGATAGTGCA‑ATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTg                                             <  2:441363/140‑1 (MQ=255)

                                                                                                      aGAACATTATGGATAGTGCA‑ATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATaa                                <  1:375867/140‑1 (MQ=255)

                                                                                                      aGAACATTATGGATAGTGCA‑ATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATATTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATaa                                >  1:501338/1‑140 (MQ=255)

                                                                                                          cATTATGGATAGTGCA‑ATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGTTATTACTTGACCTACTTGATTATTCGCTTAAAAtc                            >  1:689426/1‑140 (MQ=255)

                                                                                                           aTTATGGACAGTGCA‑ATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAAtct                           <  1:130824/140‑1 (MQ=255)

                                                                                                             tATGGATAGTGCA‑ATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCg                         <  2:657330/140‑1 (MQ=255)

                                                                                                              aTGGATAGTGCA‑ATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATTAATTCTCGc                        >  1:199279/1‑140 (MQ=255)

                                                                                                              aTGGATAGTGCA‑ATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAACTCTCGc                        >  1:688657/1‑140 (MQ=255)

                                                                                                               tGGATAGTGCA‑ATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCGTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCa                       >  2:385294/1‑140 (MQ=255)

                                                                                                                       gCA‑ATAATAATTGTTATATAATCTAACCAAATATGCATTAACCCTGTTAAAATAAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGAAATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTaaatc               >  2:202063/1‑138 (MQ=255)

                                                                                                                        cA‑ATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCt              <  1:424750/140‑1 (MQ=255)

                                                                                                                           ataataatTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGTTTATTAGCATAAAATCTCGCACTTAAAGCTTg            >  1:249335/1‑140 (MQ=255)

                                                                                                                           ataataatTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTg            >  1:4355/1‑140 (MQ=255)

                                                                                                                            taataatTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGt           <  2:596182/140‑1 (MQ=255)

                                                                                                                                  ttGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCCCTTAAAGCTTGTAAATgg     >  2:313628/1‑140 (MQ=255)

                                                                                                                                   tGTTATATAATCTCATCAAATATTCATTAACCCGGCTAAAATGCACTCTTTTGTTTGTTCAACATCATTAATAACTCCAGTTATTACTTGACCTCCTTGATTCTTTGCATAGACACACGCTTTTAAAGCTTGTAAATGGt    <  2:613946/140‑1 (MQ=255)

                                                                                                                                   tGTTATATAATCTAACCAAATATTCATTAACCCGGTTCAAAAGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTAAATGGt    >  1:686967/1‑140 (MQ=255)

                                                                                                                                     ttATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACACTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTAAATGGTTg  <  2:495326/140‑1 (MQ=255)

TTTCACGTGTCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCA‑ATAATAATTGTTATACAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTAAATGGTTG  >  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` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A