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 F191 I1 R2	32	34.5	741600	95.9%	711194	140.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP000730	2,679,462	(A)_8→7	intergenic (+334/‑55)	USA300HOU_2535 → / → cbpD	hypothetical protein/possible secretory antigen

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,679,455	0	A	.	95.8%	99.5 / ‑2.4	24	intergenic (+327/‑62)	USA300HOU_2535/cbpD	hypothetical protein/possible secretory antigen
Reads supporting (aligned to +/- strand): ref base A (0/1); new base . (11/12); total (11/13)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATCACTATGACAATTAATTGTTAAATACATGAATTTCTACATTTTATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTGTTTTCTAAAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAATATAAAAAGATACTAATTCGTTTATTAATTGCTTTTGCAGTACTTTTCTCAGCAGATTTCACTTA  >  CP000730/2679320‑2679587

ctacatATGAGAATTAATATTTAAATATCTATTTTTCAATAAATTATGAAAATATTCATTTTTATTAGTATTCAACACTTTATATGACACCTTAATTACAGTTACTTTTATTGTTGATTGCTTACTTTGTTTTCAaaaaaa                                                                                                                                 <  2:158629/136‑1 (MQ=255)

   aCTATGACAATTAATTGTTAAATACATGAATTTCTACATTTTATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTGTTTTCTaaaaaaatt                                                                                                                              >  1:13058/1‑139 (MQ=255)

   aCTATAACAATTAATAATTAAATACATGAATTACTACATTTAATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTGTTTTCTaaaaaaatt                                                                                                                              <  2:50472/141‑3 (MQ=255)

        gACAATTAATTGTTAAATACATGAATTTCTACATTTTATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTGTTTTCT‑AAAAAAATTTGTTa                                                                                                                        >  2:81980/1‑141 (MQ=255)

                    ttAAATACATGAATTTCTACATTTTATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACAAT‑ATAAAAAAAAAAAATCTGTTATCATAATTAACg                                                                                                            <  2:31449/141‑1 (MQ=255)

                       aaTACATGAATTTCTACATTTTATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTGTTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTg                                                                                                         >  1:198028/1‑141 (MQ=255)

                             tGAATTTCTACATTTTATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTGTTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATaaa                                                                                                   >  1:211701/1‑141 (MQ=255)

                              gAATTTCTACATTTTATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTGTTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATAAAg                                                                                                  <  2:356753/141‑1 (MQ=255)

                                   tCTACATTTTATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATCGTTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATAAAGaaaaa                                                                                             >  2:29089/1‑141 (MQ=255)

                                              tGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTGTTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTgg                                                                                  >  2:86448/1‑141 (MQ=255)

                                                 aaaaaTCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTGTTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGgag                                                                               <  1:155668/141‑1 (MQ=255)

                                                   aaaTCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTGTTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGAt                                                                             >  1:249025/1‑141 (MQ=255)

                                                   aaaTCCATTTTTATTACAATTCAACACTTTATATAACAACTTCATTACACGTACTTTTATTGTTTATTGCTTACATTTTATTAT‑AAAAAAATTTTTTATCATAATTAATATTAAATAAAAAAAAAAATTAACTTGGGAGAt                                                                             <  2:252319/141‑1 (MQ=255)

                                                    aaTCCATTTTTATTACAATTCAACACTTTATATGACATCTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTGTTTTAT‑AAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATa                                                                            <  2:234844/141‑1 (MQ=255)

                                                                ttaCAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTGTTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAatat                                                                >  2:357017/1‑141 (MQ=255)

                                                                                    tGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTGTTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAATATAAAAAGATACTAATTCGttt                                            <  1:315099/141‑1 (MQ=255)

                                                                                                tACAGTTACTTTTATTGTTGATTGCTTACATTGTTTTCT‑AAAAAAATTTGTTATCATACTTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAATATAAAAAGATACTAATTCGTTTATTAATTGCttt                                <  1:359388/141‑1 (MQ=255)

                                                                                                tACAGTTACTTTTATTGTTGATTGCTTACATTGTTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAATATAAAAAGATACTAATTCGTTTATTAATTGCttt                                <  1:359209/141‑1 (MQ=255)

                                                                                                                gttgATTGCTTACATTGTTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAATATAAAAAGATACTAATTCGTTTATTAATTGCTTTTGCAGTACTTTTCTca                <  1:357017/141‑1 (MQ=255)

                                                                                                                 ttgATTGCTTACATTGTTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAATATAAAAAGATACTAATTCGTTTATTAATTGCTTTTGCAGTACTTTTCTcag               <  1:179912/141‑1 (MQ=255)

                                                                                                                  tgATTGCTTACATTGTTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAATATAAAAAGATACTAATTCGTTTATTAATTGCTTTTGCAGTACTTTTCTcagc              >  1:289714/1‑141 (MQ=255)

                                                                                                                  tgATTGCTTACATTGTTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAATATAAAAAGATACTAATTCGTTTATTAATTGCTTTTGCAGTACTTTTCTcagc              >  2:136789/1‑141 (MQ=255)

                                                                                                                   gATTGCTTACATTGTTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAATATAAAAAGATACTAATTCGTTTATTAATTGCTTTTGCAGTACTTTTCTcagca             <  2:249025/141‑1 (MQ=255)

                                                                                                                      tGCTTACATTGTTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAATATAAAAAGATACTAATTCGTTTATTAATTGCTTTTGCAGTACTTTTCTCAGCAGAt          <  1:79864/141‑1 (MQ=255)

                                                                                                                        cTTACATTGTTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAATATAAAAAGATACTAATTCGTTTATTAATTGCTTTTGCAGTACTTTTCTCAGCAGAttt        >  2:61127/1‑141 (MQ=255)

                                                                                                                            cATTGTTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAATATAAAAAGATACTAATTCGTTTATTAATTGCTTTTGCAGTACTTTTCTCAGCAGATTTCACt    >  2:230392/1‑141 (MQ=255)

                                                                                                                              ttGTTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAATATAAAAAGATACTAATTCGTTTATTAATTGCTTTTGCAGTACTTTTCTCAGCAGATTTCACTTa  <  2:28290/141‑1 (MQ=255)

ATCACTATGACAATTAATTGTTAAATACATGAATTTCTACATTTTATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTGTTTTCTAAAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAATATAAAAAGATACTAATTCGTTTATTAATTGCTTTTGCAGTACTTTTCTCAGCAGATTTCACTTA  >  CP000730/2679320‑2679587

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