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
A3 F121 I1 R2	9	39.2	904072	90.0%	813664	139.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP000730	2,610,079	(T)_7→8	coding (447/795 nt)	USA300HOU_2473 ←	lipoprotein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,610,072	1	.	T	80.8%	67.1 / 13.8	26	coding (454/795 nt)	USA300HOU_2473	lipoprotein
Reads supporting (aligned to +/- strand): ref base . (0/5); new base T (9/12); total (9/17)
Fisher's exact test for biased strand distribution p-value = 1.29e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.29e-01

ACATTATAATCATCATTATTCAATTGATATTTTGCCGAATAACTTGGTACATTAGGATTATATGAAATATCACCATCTTTATAATCATTAATATCTTTAAAGTTGCCATATTGTACAAAGAACTTAAAGTTTTCAATCTC‑TTTTTTTAACTTGTCATTCGGTAGTGGCTTCGTTGGTATGATTTTATTATGTTCCATTTTTACCGGATACCTTTTTTCATCATCCTTTGGTCTGCCGTTACTGTCATCTGTCATTTCACTTATAAAATAATACC  >  CP000730/2609933‑2610206

aCATTATAATCATCATTATTCAATTGATATTTTGCCGAATAACTTGGTACATTAGGATTATATGAAATATCACCATCTTTATAATCATTAATATCTTTAAAGTTGCCATATTGTACAAAGAACTTAAAGTTTTCAATctc‑t                                                                                                                                       <  1:401261/141‑1 (MQ=255)

 cATTATAATCATCATTATTCAATTGATATTTTGCCGAATAACTTGGTACATTAGGATTATATGAAATATCACCATCTTTATAATCATTAATATCTTTAAAGTTGCCATATTGTACAAAGAACTTAAAGTTTTCAATCTC‑tt                                                                                                                                      >  1:129186/1‑141 (MQ=255)

                tattCAATTGATATTTTGCCGAATAACTTGGTACATTAGGATTATATGAAATATCACCATCTTTATAATCATTAATATCTTTAAAGTTGCCATATTGTACAAAGAACTTAAAGTTTTCAATCTCTTTTTTTTAACTTGTCa                                                                                                                        <  1:443134/141‑1 (MQ=255)

                 attCAATTGATATTTTGCCGAATAACTTGGTACATTAGGATTATATGAAATATCACCATCTTTATAATCATTAATATCTTTAAAGTTGCCATATTGTACAAAGAACTTAAAGTTTTCAATCTCTTTTTTTTAACTTGTCAt                                                                                                                       <  1:285014/141‑1 (MQ=255)

                      aTTGATATTTTGCCGAATAACTTGGTACATTAGGATTATATGAAATATCACCATCTTTATAATCATTAATATCTTTAAAGTTGCCATATTGTACAAAGAACTTAAAGTTTTCAATCTCTTTTTTTTAACTTGTCATTCGGt                                                                                                                  <  2:211122/141‑1 (MQ=255)

                          atatTTTGCCGAATAACTTGGTACATTAGGATTATATGAAATATCACCATCTTTATAATCATTAATATCTTTAAAGTTGCCATATTGTACAAAGAACTTAAAGTTTTCAATCTC‑TTTTTTTAACTTGTCATTCGGTAGTgg                                                                                                             <  1:162135/141‑1 (MQ=255)

                                      aTAACTTGGTACATTAGGATTATATGAAATATCACCATCTTTATAATCATTAATATCTTTAAAGTTGCCATATTGTACAAAGAACTTAAAGTTTTCAATCTCTTTTTTTTTTTTTTTTATTTGGTAGTGGCTTCGTTgttt                                                                                                  >  2:253437/1‑138 (MQ=17)

                                      aTAACTTGGTACATTAGGATTATATGAAATATCACCATCTTTATAATCATTAATATCTTTAAAGTTGCCATATTGTACAAAGAACTTAAAGTTTTCAATCTCTTTTTTTTAACTTGTCATTCGGTAGTGGCTTCGTTGGTa                                                                                                  >  1:48742/1‑141 (MQ=255)

                                        aaCTTGGTACATTAGGATTATATGAAATATCACCATCTTTATAATCATTAATATCTTTAAAGTTGCCATATTGTACAAAGAACTTAAAGTTTTCAATCTCTTTTTTTTAACTTGTCATTCGGTAGTGGCTTCGTTGGTATg                                                                                                <  1:52260/141‑1 (MQ=255)

                                              gTACATTAGGATTATATGAAATATCACCATCTTTATAATCATTAATATCTTTAAAGTTGCCATATTGTACAAAGAACTTAAAGTTTTCAATCTCTTTTTTTTAACTTGTCATTCGGTAGTGGCTTCGTTGGTATGATTtta                                                                                          <  1:1073/141‑1 (MQ=255)

                                                  aTTAGGATTATATGAAATATCACCATCTTTATAATCATTAATATCTTTAAAGTTGCCATATTGTACAAAGAACTTAAAGTTTTCAATCTCTTTTTTTTAACTTGTCATTCGGTAGTGGCTTCGTTGGTATGATTTtattat                                                                                      <  2:178622/141‑1 (MQ=255)

                                                    tAGGATTATATGAAATATCACCATCTTTATAATCATTAATATCTTTAAAGTTGCCATATTGTACAAAGAACTTAAAGTTTTCAATCTC‑TTTTTTTAACTTGTCATTCGGTAGTGGCTTCGTTGGTATGATTTTATTATGtt                                                                                   <  2:392288/141‑1 (MQ=255)

                                                                     tCACCATCTTTATAATCATTAATATCTTTAAAGTTGCCATATTGTACAAAGAACTTAAAGTTTTCAATCTCTTTTTTTTTTTTTTTCATTCGGTAGTGGCTTCGTTGGTATGATTTTATTATGTTCCATTTTTACCGGATa                                                                   >  2:2471/1‑141 (MQ=25)

                                                                     tCACCATCTTTATAATCATTAATATCTTTAAAGTTGCCATATTGTACAAAGAACTTAAAGTTTTCAATCTCTTTTTTTTAACTTGTCATTCGGTAGTGGCTTCGTTGGTATGATTTTATTATGTTCCATTTTTACCGGATa                                                                   >  1:180296/1‑141 (MQ=255)

                                                                           tCTTTATCATCATTAATATCTTTAAAGTTGCCATATTGTACAAAGAACTTAAAGTTTTCAATCTCTTTTTTTTAACTTGTCATTCGGTAGTGGCTTCGTTTGTATGATTTTATTATGTTCCATTTTTGCCGGACACCtttt                                                             <  2:197003/141‑1 (MQ=21)

                                                                                 taATCATTAATATCTTTAAAGTTGCCATATTGTACAAAGAACTTAAAGTTTTCAATCTCTTTTTTTTAACTTGTCATTCGGTAGTGGCTTCGTTGGTATGATTTTATTATGTTCCATTTTTACCGGATACCTTTTTtcatc                                                       >  1:46094/1‑141 (MQ=255)

                                                                                                    aGTTGCCATATTGTACAAAGAACTTAAAGTTTTCAATCTCTTTTTTTTAACTTGTCATTCGGTAGTGGCTTCGTTGGTATGATTTTATTATGTTCCATTTTTACCGGATACCTTTTTTCATCATCCTTTGGTCTGCCGTTa                                    <  2:381248/141‑1 (MQ=255)

                                                                                                     gTTGCCATATTGTACAAAGAACTTAAAGTTTTCAATCTC‑‑TTTTTTAACTTGTCATTCGGTAGTGGCTTCGTTGGTATGATTTTATTATGTTCCATTTTTACCGGATACCTTTTTTCATCATCCTTTGGTCTGCCGTTActg                                 <  2:316643/141‑1 (MQ=255)

                                                                                                      ttGCCATATTGTACAAAGAACTTAAAGTTTTCAATCTC‑TTTTTTTAACTTGTCATTCGGTAGTGGCTTCGTTGGTATGATTTTATTATGTTCCATTTTTACCGGATACCTTTTTTCATCATCCTTTGGTCTGCCGTTActg                                 <  1:410258/141‑1 (MQ=255)

                                                                                                              ttGTACAAAGAACTTAAAGTTTTCAATCTCTTTTTTTTAACTTGTCATTCGGTAGTGGCTTCGTTGGTATGATTTTATTATGTTCCATTTTTACCGGATACGTTTTTTCATCATCCTTTGGTCTGCCGTTActgtcatctg                          <  2:375463/141‑1 (MQ=255)

                                                                                                                  aCAAAGAACTTAAAGTTTTCAATCTCTTTTTTTTAACTTGTCATTCGGTAGTGGCTTCGTTGGTATGATTTTATTATGTTCCATTTTTACCGGATACCTTTTTTCATCTTCCTTTGGTCTGCCGTTActgtcatctgtcat                      >  2:138453/1‑141 (MQ=255)

                                                                                                                             aaaGTTTTCAATCTCTTTTTTTTAACTTGTCATTCGGTAGTGGCTTCGTTGGTATGATTTTATTATGTTCCATTTTTACCGGATACCTTTTTTCATCATCCTTTGGTCTGCCGTTACTGTCATCTGTCATTTCACTTATaa           >  1:144126/1‑141 (MQ=255)

                                                                                                                              aaGTTTTCAATCTCTTTTTTTTAACTTGTCATTCGGTAGTGGCTTCGTTGGTATGATTTTATTATGTTCCATTTTTACCGGATACCTTTTTTCATCATCCTTTGGTCTGCCGTTACTGTCATCTGTCATTTCACTTATaaa          >  1:228640/1‑141 (MQ=255)

                                                                                                                                   ttCAATCTCTTTTTTTTAACTTGTCATTCGGTAGTGGCTTCGTTGGTATGATTTTATTATGTTCCATTTTTACCGGATACCTTTTTTCATCATCCTTTGGTCTGCCGTTACTGTCATCTGTCATTTCACTTATAAaataat     <  1:83517/141‑1 (MQ=255)

                                                                                                                                    tCAATCTCTTTTTTTTAATTTGTCATTCGGTAGTGGCTTCGTTGGTATGATTTTATTATGTTCCATTTTTACCGGATACCTTTTTTCATCATCCTTTGGTCTGCCGTTACTTTCATTTTTCATTTCACTTTTAAAataata    >  2:309275/1‑141 (MQ=255)

                                                                                                                                     cAATCTCTTTTTTTTAACTTGTCATTCGGTAGTGGCTTCGTTGGTATGATTTTATTATGTTCCATTTTTACCGGATACCTTTTTTCATCATCCTTTGGTCTGCCGTTACTGTCATCTGTCATTTCACTTATAAAATAATAc   <  2:48742/141‑1 (MQ=255)

                                                                                                                                     cAATCTC‑TTTTTTTAACTTGTCATTCGGTAGTGGCTTCGTTGGTATGATTTTATTATGTTCCATTTTTACCGGATACCTTTTTTCATCATCCTTTGGTCTGCCGTTACTGTCATCTGTCATTTCACTTATAAAATAATAcc  <  2:398951/141‑1 (MQ=255)

                                                                                                                                      aaTCTCTTTTTTTTAACTTGTCATTCGGTAGTGGCTTCGTTGGTATGATTTTATTATGTTCCATTTTTACCGGATACCTTTTTTCATCATCCTTTGGTCTGCCGTTACTGTCATCTGTCATTTCACTTATAAAATAATAcc  <  1:230008/141‑1 (MQ=255)

ACATTATAATCATCATTATTCAATTGATATTTTGCCGAATAACTTGGTACATTAGGATTATATGAAATATCACCATCTTTATAATCATTAATATCTTTAAAGTTGCCATATTGTACAAAGAACTTAAAGTTTTCAATCTC‑TTTTTTTAACTTGTCATTCGGTAGTGGCTTCGTTGGTATGATTTTATTATGTTCCATTTTTACCGGATACCTTTTTTCATCATCCTTTGGTCTGCCGTTACTGTCATCTGTCATTTCACTTATAAAATAATACC  >  CP000730/2609933‑2610206

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A