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
A19 F74 I0 R1	21	36.7	824702	95.0%	783466	140.9

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%	110.9 / NA	36	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 (20/16); total (20/16)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CTTTCACGTGTCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATACAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTA  >  USA300TCH1516_ALE/2010225‑2010489

cTTTCACGTGTCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAATGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATaa                                                                                                                              >  2:357037/1‑141 (MQ=255)

  tttccGTGTCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTTAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATc                                                                                                                            <  1:122653/137‑1 (MQ=255)

  ttCACGTGTCAATTTTCTTAAACTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATAAAAAGTGCAATTATAATTGTTATATAATc                                                                                                                            <  2:206337/141‑1 (MQ=255)

    cACGTGTCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTa                                                                                                                          >  1:146616/1‑141 (MQ=255)

     aCGTGTCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTaa                                                                                                                         >  1:249038/1‑141 (MQ=255)

               tttCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTc                                                                                                               >  1:235527/1‑141 (MQ=255)

                  cTTAGTCTTCCAAAGAAAACGTACACCGTTCAAATGTAAAGTTTGAAGATAAACATTGCTGCTAAAGTCATTTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAAGTTACCTAAATATACAtt                                                                                                            >  2:304934/1‑141 (MQ=255)

                      aTCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAAcc                                                                                                        <  2:392051/141‑1 (MQ=255)

                       tCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAAccc                                                                                                       >  2:61157/1‑141 (MQ=255)

                               aGAAAACGTACACCGTTAAAATGTAAAATGGAAAGATAAACAGTGCTGGTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTaaaa                                                                                               >  1:262017/1‑141 (MQ=255)

                                 aaaaCGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATg                                                                                             <  1:17246/141‑1 (MQ=255)

                                  aaaCGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGa                                                                                            <  1:330592/141‑1 (MQ=255)

                                    aCGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGaaa                                                                                          <  1:66403/141‑1 (MQ=255)

                                     cGTACACCGTTAAAATGTAAAATGGGAAGAAAAACCATAGAGCTAAAATAAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATATTAAAAGAGATATAATATAACCAAATATTCATTAACCCAGTTAAAATCaatt                                                                                         >  2:68009/1‑139 (MQ=255)

                                                aaaatgtaaaatgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTttgtttgt                                                                              <  1:324713/141‑1 (MQ=255)

                                                          atgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAAcatcat                                                                    <  1:293382/141‑1 (MQ=255)

                                                                    aaaCAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAAGATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCAGTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCActct                                                          <  1:68009/141‑1 (MQ=255)

                                                                    aaaCAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACACAGTTAAAATGAATTATTTTGTTTGTTAATCATAATTAATCAcacc                                                          >  2:221030/1‑138 (MQ=255)

                                                                       cAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGa                                                       >  1:45056/1‑141 (MQ=255)

                                                                                tAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTg                                              <  1:213330/141‑1 (MQ=255)

                                                                                 aaaGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGa                                             >  1:137173/1‑141 (MQ=255)

                                                                                       aaTTTCACATATAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACt                                       <  2:380731/141‑1 (MQ=255)

                                                                                        aTTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACtt                                      >  2:319675/1‑141 (MQ=255)

                                                                                        aTTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAAACCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGCTATTACTTGACCTACtt                                      >  2:180920/1‑141 (MQ=255)

                                                                                            cacaTCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGatt                                  >  2:280526/1‑141 (MQ=255)

                                                                                            cacaTCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGatt                                  >  1:259960/1‑141 (MQ=255)

                                                                                                        gAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACAAAATATTCTTTACCCCGTTTAAAATAAAATCTTTTGTTTGTTAAACATATTTGATGAGTTTAATTATTACTTGACTTACTTGATTTTTAGCATaaaa                      >  1:320018/1‑141 (MQ=255)

                                                                                                           cATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAAtct                   >  1:286287/1‑141 (MQ=255)

                                                                                                           cATTATGGATAGTGCAATAATAATTGTTATATAATCTAAACAAATATTCATTAACCCGGTTAAAATGAAATGTTGTGTTTGTTCAACATCATTAATTACTCTAGAAATTAATTGACCTACTTGAGTATTATCCTAAAAttt                   >  2:261568/1‑139 (MQ=255)

                                                                                                             ttATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCg                 >  2:125046/1‑141 (MQ=255)

                                                                                                              tATGGATAGTGCAATAATAATTGCTATATAATCTACCCAAATATTCATTAACCCTGTTAAAATGAAATCTTTTGTTTGTTCAACATCCTTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGc                <  1:55415/141‑1 (MQ=255)

                                                                                                               agggATAGTGCAATAATAAGTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCa               <  2:119458/139‑1 (MQ=255)

                                                                                                                 ggATAGTGAAATAATAATTGTTATATAATCTAATCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACt             <  2:107122/141‑1 (MQ=255)

                                                                                                                     aGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAAATATTACTTGACCTACTTGATTATTAGAATAAAATCTCGCACTTaaa         >  2:32219/1‑141 (MQ=255)

                                                                                                                          aataataatTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTg    <  2:125141/141‑1 (MQ=255)

                                                                                                                            taataatTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTa  <  2:137173/141‑1 (MQ=255)

CTTTCACGTGTCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATACAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTA  >  USA300TCH1516_ALE/2010225‑2010489

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