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
A13 F68 I1 R1	13	30.2	709236	94.0%	666681	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	2,010,363	C→T	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%	81.1 / NA	26	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 (8/18); total (8/18)

CGTGTCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATACAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTG  >  USA300TCH1516_ALE/2010231‑2010487

cGTGTCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAACATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGTAATAATAATTGTTATATAATCTaaa                                                                                                                      >  2:56072/1‑140 (MQ=255)

cGTGTCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAAc                                                                                                                      <  1:147952/141‑1 (MQ=255)

cGTGTCAATTTTCGTAATCTGCCAAAGAAAGCGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAAc                                                                                                                      <  1:65531/141‑1 (MQ=255)

  tgtCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCa                                                                                                                    <  2:213250/141‑1 (MQ=255)

          ttCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCa                                                                                                            <  2:201334/141‑1 (MQ=255)

                aTCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAAcc                                                                                                      >  1:40038/1‑141 (MQ=255)

                         aGAAAACGTACAGCGTTAAAATGAAAAAGGGGAAGATAAACAGTGCTGCTAAAGTCAAATTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTaaaa                                                                                             <  1:31996/141‑1 (MQ=255)

                          gAAAACGTAGACAGTTAAAATGTGAAAAGGGGAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTTAAAAGAACATTAAGTATAGTGCAATAATAAGTGTTATATGATCTATGCAAATATTCATTAACCCGGTTAAAAt                                                                                            <  2:155687/141‑1 (MQ=255)

                           aaaaCGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATg                                                                                           <  1:266435/141‑1 (MQ=255)

                                gTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATc                                                                                      >  1:123663/1‑141 (MQ=255)

                                          aaaatgtaaaatgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGTATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTttgtttgt                                                                            <  2:214364/141‑1 (MQ=255)

                                          aaaatgtaaaatgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTttgtttgt                                                                            <  1:158546/141‑1 (MQ=255)

                                            aatgtaaaatgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGCTCCTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTc                                                                          <  1:49344/141‑1 (MQ=255)

                                            aatgtaaaatgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTc                                                                          <  1:341633/141‑1 (MQ=255)

                                                       ggAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTaa                                                               >  1:194916/1‑141 (MQ=255)

                                                          aGATAATGAGTGCTGCTAAAGTCAATTTTACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAACCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCa                                                            <  2:280452/141‑1 (MQ=255)

                                                                      ctgctAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTa                                                <  1:236055/141‑1 (MQ=255)

                                                                            aaGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGAc                                          <  1:337905/141‑1 (MQ=255)

                                                                                cAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTAc                                      <  1:14648/141‑1 (MQ=255)

                                                                                 aaTTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACt                                     >  1:234264/1‑141 (MQ=255)

                                                                                             aaaaaGAACATTACGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCa                         <  1:56072/141‑1 (MQ=255)

                                                                                                  gAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATaaaa                    >  1:181701/1‑141 (MQ=255)

                                                                                                                gttcAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAg      <  2:109768/138‑1 (MQ=255)

                                                                                                                gTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAg      <  2:151123/141‑1 (MQ=255)

                                                                                                                   cAATAATAATTCTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTTACTCATTTGATTATTAGCATAAACTCTCGCCCTTTAAGCtt   >  2:153042/1‑141 (MQ=255)

                                                                                                                    aataataatTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTAATTTACCTACTTGATTATTAGCATAAAAACTCGCACTAACAGCTTg  >  2:269021/1‑141 (MQ=255)

CGTGTCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATACAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTG  >  USA300TCH1516_ALE/2010231‑2010487

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