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
A1 F169 I1 R1	62	44.4	970160	98.1%	951726	147.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	1,932,853	T→C	I799V (ATT→GTT)	USA300HOU_RS09605 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,932,853	0	T	C	100.0%	131.6 / NA	35	I799V (ATT→GTT)	USA300HOU_RS09605	hypothetical protein
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (20/15); total (20/15)

ATTAGATATATCTTTTGATAAACTAATATATTCAATTGTTTGCCTAGCATAATCTCTCATTAAAATATGAGGATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAAATGTCGATTCGAAGTGTCGCCCCTAAAACAGAAGCATATAATCTTTCGACTATATATGGATCATTGTTATTTTCAAATAATTTTAATAAACCAATAATTTTAGTTGGAAATGTTTTGAATAATTTTACTAAAGATTTAGTAC  >  USA300TCH1516_ALE/1932713‑1932993

atTAGATATATCTTTTGATAAACTAATATATTCAATTGTTTGCCTAGCATAATCTCTCATTAAAATATGAGGATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAAACGTCGAtt                                                                                                                                       <  3:120430/148‑1 (MQ=255)

atTAGATATATCTTTTGATAAACTAATATATTCAATTGTTTGCCTAGCATAATCTCTCATTAAAATATGAGGATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAAACGTCGAtt                                                                                                                                       <  3:319766/148‑1 (MQ=255)

        tatCTTTTGATAAACTAATATATTCAATTGTTTGCCTAGCATAATCTCTCATTAAAATATGAGGATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAAACGTCGATTCGAAgtgt                                                                                                                               <  4:43169/148‑1 (MQ=255)

          tCTTTTGATAAACTAATATATTCAATTGTTTGCCTAGCATAATCTCTCATTAAAATATGAGGATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAAACGTCGATTCGAAGTGTCg                                                                                                                             >  3:170721/1‑148 (MQ=255)

          tCTTTTGATAAACTAATATATTCAATTGTTTGCCTAGCATAATCTCTCATTAAAATATGAGGATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAAACGTCGATTCGAAGTGTCg                                                                                                                             >  3:400278/1‑148 (MQ=255)

          tCTTTTGATAAACTAATATATTCAATTGTTTGCCTAGCATAATCTCTCATTAAAATATGAGGATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAAACGTCGATTCGAAGTGTCg                                                                                                                             >  4:236312/1‑148 (MQ=255)

                      cTAATATATTCAATTGTTTGCCTAGCATAATCTCTCATTAAAATATGAGGATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAAACGTCGATTCGAAGTGTCGCCCCTAAAACAg                                                                                                                 <  4:109603/148‑1 (MQ=255)

                       tAATATATTCAATTGTTTGCCTAGCATAATCTCTCATTAAAATATGAGGATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAAACGTCGATTCGAAGTGTCGCCCCTAAAACAGa                                                                                                                <  3:262602/148‑1 (MQ=255)

                               tCAATTGTTTGCCTAGCATAATCTCTCATTAAAATATGAGGATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAAACGTCGATTCGAAGTGTCGCCCCTAAAACAGAAGCAtata                                                                                                        <  4:153340/148‑1 (MQ=255)

                               tCAATTGTTTGCCTAGCATAATCTCTCATTAAAATATGAGGATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAAACGTCGATTCGAAGTGTCGCCCCTAAAACAGAAGCAtata                                                                                                        <  4:135779/148‑1 (MQ=255)

                               tCAATTGTTTGCCTAGCATAATCTCTCATTAAAATATGAGGATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAAACGTCGATTCGAAGTGTCGCCCCTAAAACAGAAGCAtata                                                                                                        <  3:380351/148‑1 (MQ=255)

                                   ttGTTTGCCTAGCATAATCTCTCATTAAAATATGAGGATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAAACGTCGATTCGAAGTGTCGCCCCTAAAACAGAAGCATATAATCt                                                                                                    <  3:384391/148‑1 (MQ=255)

                                                                 tatGAGGATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAAACGTGGAGTCGAGGTGGCGCACCTAAAACAGAAGCATATAATCTTTCGACTATATATGGATCATTGTTATTTTc                                                                      >  3:248344/1‑148 (MQ=255)

                                                                 tatGAGGATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAAACGTCGATTCGAAGTGTCGCCCCTAAAACAGAAGCATATAATCTTTCGACTATATATGGATCATTGTTATTTTc                                                                      >  3:348931/1‑148 (MQ=255)

                                                                 tatGAGGATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAAACGTCGATTCGAAGTGTCGCACCTAAAACAGAAGCATATAATCTTTCGACTATATATGGATCATTGTTATTTTc                                                                      >  3:248368/1‑148 (MQ=255)

                                                                  atGAGGATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAGACGTCGATTCGAAGTGTCGCCCCTAAAACAGAAGCATATAATCTTTCGACTATATATGGATCATTGTTATTTTCa                                                                     >  3:179994/1‑148 (MQ=255)

                                                                  atGAGGATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAAACGTCGATTCGAAGTGTCGCCCCTAAAACAGAAGCATATAATCTTTCGACTATATATGGATCATTGTTATTTTCa                                                                     >  3:344198/1‑148 (MQ=255)

                                                                         tataCCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAAACGTCGATTCGAAGTGTCGCCCCTAAAACAGAAGCATATAATCTTTCGACTATATATGGATCATTGTTATTTTCAAATAAtt                                                              >  4:382941/1‑148 (MQ=255)

                                                                         tataCCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAAACGTCGATTCGAAGTGTCGCCCCTAAAACAGAAGCATATAATCTTTCGACTATATATGGATCATTGTTATTTTCAAATAAtt                                                              <  4:74853/148‑1 (MQ=255)

                                                                               aTTTCTTTATCAAATATTTCTTCATAAATATAATTAGCACTCTCTATATGTATTTCACAAACGTCGATTCGAAGTGTCGCCCCTAAAACAGAAGCATATAATCTTTCGACTATATATGTATCATTGTTATTTTCAAATAATTTtaata                                                        >  4:137129/1‑148 (MQ=255)

                                                                                   cTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAAACGTCGATTCGAAGTGTCGCCCCTAAAACAGAAGCATATAATCTTTCGACTATATATGGATCATTGTTATTTTCAAATAATTTTAATAAAcc                                                    <  4:176686/148‑1 (MQ=255)

                                                                                        tCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAAACGTCGATTCGAAGTGTCGCCCCTAAAACAGAAGCATATAATCTTTCGACTATATATGGATCATTGTTATTTTCAAATAATTTTAATAAACCaataa                                               <  3:71359/148‑1 (MQ=255)

                                                                                                        aaaTATAATTAGCAATCTCTATATGTATTTCACAAACGTCGATTCGAAGTGTCGCCCCTAAAACAGAAGCATATAATCTTTCGACTATATATGGATCATTGTTATTTTCAAATAATTTTAATAAACCAATAATTTTAGTTGGAAATGt                               <  3:403969/148‑1 (MQ=255)

                                                                                                        aaaTATAATTAGCAATCTCTATATGTATTTCACAAACGTCGATTCGAAGTGTCGCCCCTAAAACAGAAGCATATAATCTTTCGACTATATATGGATCATTGTTATTTTCAAATAATTTTAATAAACCAATAATTTTAGTTGGAAATGt                               <  4:191720/148‑1 (MQ=255)

                                                                                                               aTTAGCAATCTCTATATGTATTTCACAAACGTCGATTCGAAGTGTCGCCCCTAAAACAGAAGCATATAATCTTTCGACTATATATGGATCATTGTTATTTTCAAATAATTTTAATAAACCAATAATTTTAGTTGGAAATGTTTTGaat                        >  4:368242/1‑148 (MQ=255)

                                                                                                               aTTAGCAATCTCTATATGTATTTCACAAACGTCGATTCGAAGTGTCGCCCCTAAAACAGAAGCATATAATCTTTCGACTATATATGGATCATTGTTATTTTCAAATAATTTTAATAAACCAATAATTTTAGTTGGAAATGTTTTGaat                        >  4:9434/1‑148 (MQ=255)

                                                                                                                 tAGCAATCTCTATATGTATTGCACAAACGTCGATTCGAAGTGTCGCCCCTAAAACAGAAGCATATAATCTTTCGACTATATATGGATCATTGTTATTTTCAAATAATTTTAATAAACCAATAATTTTAGTTGGAAATGTTTTGaataa                      <  4:28163/148‑1 (MQ=255)

                                                                                                                    cAATCACTATATGTATTTCACAAACGTCGATTCGAAGTGTCGCCCCTAAAACAGAAGCATATAATCTTTCGACTATATATGGATCATTGTTATTTTCAAATAATTTTAATAAACCAATAATTTTAGTTGGAACTGTTTTGAATAAttt                   >  3:345663/1‑148 (MQ=255)

                                                                                                                      aTCTCTATATGTATTTCACAAACGTCGATTCGAAGTGTCGCCCCTAAAACAGAAGCATATAATCTTTCGACTATATATGGATCATTGTTATTTTCAAATAATTTTAATAAACCAATAATTTTAGTTGGAAATGTTTTGAATAATTTTa                 >  3:306237/1‑148 (MQ=255)

                                                                                                                      aTCTCTATATGTATTTCACAAACGTCGATTCGAAGTGTCGCCCCTAAAACAGAAGCATATAATCTTTCGACTATATATGGATCATTGTTATTTTCAAATAATTTTAATAAACCAATAATTTTAGTTGGAAATGTTTTGAATAATTTTa                 >  3:275562/1‑148 (MQ=255)

                                                                                                                                gTATTTCACAAACGTCGATTCGAAGTGTCGCCCCTAAAACAGAAGCATATAATCTTTCGACTATATATGGATCATTGTTATTTTCAAATAATTTTAATAAACCAATAATTTTAGTTGGAAATGTTTTGAATAATTTTACTAAAGAttt       >  4:47984/1‑148 (MQ=255)

                                                                                                                                gTATTTCACAAACGTCCATTCGAAGTGTCGCCCCTAAAACAGAAGCATATAATCTTTCGACTATATATGGATCATTGTTATTTTCAAATAATTTTAATAAACCAATAATTTTAGTTGGAAATGTTTTGAATAATTTTACTAAAGAttt       >  3:365839/1‑148 (MQ=255)

                                                                                                                                   tttCACAAACGTCGATTCGAAGTGTCGCCCCTAAAACAGAAGCATATAATCTTTCGACTATATATGGATCATTGTTATTTTCAAATAATTTTAATAAACCAATAATTTTAGTTGGAAATGTTTTGAATAATTTTACTAAAGATTTAGt    >  4:360176/1‑148 (MQ=255)

                                                                                                                                   tttCACAAACGTCGATTCGAAGTGTCGCCCCTAAAACAGAAGCATATAATCTTTCGACTATATATGGATCATTGTTATTTTCAAATAATTTTAATAAACCAATAATTTTAGTTGGAAATGTTTTGAATAATTTTACTAAAGATTTAGt    >  4:75883/1‑148 (MQ=255)

                                                                                                                                     tCACAAACGTCGATTCGAAGTGTCGCCCCTAAAACAGAAGCATATAATCTTTCGACTATATATGGATCATTGTTATTTTCAAATAATTTTAATAAACCAATAATTTTAGTTGGAAATGTTTTGAATAATTTTACTAAAGATTTAGTAc  >  4:32791/1‑148 (MQ=255)

ATTAGATATATCTTTTGATAAACTAATATATTCAATTGTTTGCCTAGCATAATCTCTCATTAAAATATGAGGATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAAATGTCGATTCGAAGTGTCGCCCCTAAAACAGAAGCATATAATCTTTCGACTATATATGGATCATTGTTATTTTCAAATAATTTTAATAAACCAATAATTTTAGTTGGAAATGTTTTGAATAATTTTACTAAAGATTTAGTAC  >  USA300TCH1516_ALE/1932713‑1932993

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A