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
A21 F42 I0 R1	24	30.6	687070	95.0%	652716	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%	95.6 / NA	31	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 (15/16); total (15/16)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

ATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATACAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTAAATGGTTGTAT  >  USA300TCH1516_ALE/2010238‑2010500

aTTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTCCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAatat                                                                                                                            >  2:277915/1‑141 (MQ=255)

              ccAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGtt                                                                                                              >  1:85499/1‑141 (MQ=255)

               cAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTa                                                                                                             <  1:100536/141‑1 (MQ=255)

                   aaaaaCGAACACAGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAAt                                                                                                         <  2:162991/140‑1 (MQ=255)

                    aaaaCGTACGCCATTGTAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCGAAAAAGAACATTATGTATAGGGTGATAATAATAGTTAGATAATCTAACCAAATATTCATTAACCCGGTTAAAATg                                                                                                        <  2:140404/141‑1 (MQ=255)

                      aaCGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGaa                                                                                                      >  1:196288/1‑141 (MQ=255)

                        cGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAAt                                                                                                    >  2:220104/1‑141 (MQ=255)

                        cGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAAt                                                                                                    >  1:60462/1‑141 (MQ=255)

                                        gtaaaatgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAAc                                                                                    >  1:273921/1‑141 (MQ=255)

                                              tgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCAtt                                                                              <  1:56550/141‑1 (MQ=255)

                                                    gATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAACAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCAc                                                                        <  1:51807/141‑1 (MQ=255)

                                                           aGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGat                                                                 <  1:57461/141‑1 (MQ=255)

                                                              gctgctAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATAtt                                                              >  2:303775/1‑141 (MQ=255)

                                                              gctgctAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATAtt                                                              >  1:235671/1‑141 (MQ=255)

                                                                  ctAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACtt                                                          >  1:230302/1‑141 (MQ=255)

                                                                  atAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACtt                                                          <  2:329226/140‑1 (MQ=255)

                                                                   tAAAGGCAATATCACATCTACAGAGAACATGAGGGATAGTGCAATAACAATTGTTGTATAATCTATCCAAATATTCATGAACCCGATTCACTTGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTg                                                         <  2:334006/141‑1 (MQ=255)

                                                                    aaaGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGa                                                        <  1:317587/141‑1 (MQ=255)

                                                                     aaGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTAAATAACCCTGTTGGCTCGCCATCAGTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGAc                                                       <  2:156022/141‑1 (MQ=255)

                                                                       gTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCt                                                     <  2:163610/141‑1 (MQ=255)

                                                                            tttCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTTAATATTACTTGACCTACttt                                                >  2:321604/1‑140 (MQ=255)

                                                                               cacaTCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGatt                                             >  1:330403/1‑141 (MQ=255)

                                                                                           gAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATaaaa                                 <  2:172468/141‑1 (MQ=255)

                                                                                                   tGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCAc                         <  1:151467/141‑1 (MQ=255)

                                                                                                     gATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACtt                       >  2:108503/1‑141 (MQ=255)

                                                                                                     gATAGTGAAATAATAATTGTTATATAATCTAATCAAATATTCATTCACCCTGTTCTTACGCGTGCTCTTCTTTTTTATACTGCTGTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCAGAAAATCTCGCACtt                       <  2:243927/141‑1 (MQ=255)

                                                                                                          tGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGc                  <  1:303775/141‑1 (MQ=255)

                                                                                                           gCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGCTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAACATCTCACACTTAAAGCt                 >  2:156824/1‑141 (MQ=255)

                                                                                                               taataatTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTa             <  1:27541/141‑1 (MQ=255)

                                                                                                                    atTGTTATATAATCTAACCAAATATTCATTAACACGATTAAAATGAAAGAGTTTGTTCCTCCAACTGCATTAATCACTCTAGATATTACTTGACATACTTGATTATTAGCATAAAATCTCGCAATTAAAGCTTGTAAATgg        >  2:124086/1‑141 (MQ=255)

                                                                                                                     ttGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTAAATGGt       >  1:14860/1‑141 (MQ=255)

                                                                                                                          atatAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAATATCTCGCACTTAAAGCTTGTAAATGGTTGtat  <  2:303369/141‑1 (MQ=255)

ATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATACAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTAAATGGTTGTAT  >  USA300TCH1516_ALE/2010238‑2010500

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