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
A15 F116 I0 R1	44	26.4	562224	96.5%	542546	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	1,274,212	A→T	58.8%	K205N (AAA→AAT)	USA300HOU_1186 →	CodY family transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,274,212	0	A	T	58.8%	16.2 / 29.9	29	K205N (AAA→AAT)	USA300HOU_1186	CodY family transcriptional regulator
Reads supporting (aligned to +/- strand): ref base A (3/9); new base T (10/7); total (13/16)
Fisher's exact test for biased strand distribution p-value = 1.30e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTAGAAAAAGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTAAAGTTAAAAAAGAAAAATTCTTAG  >  CP000730/1274081‑1274348

cgaGAAAAAGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTCATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTATTCGCATCAAATGTTGCAGAt                                                                                                                                 <  1:196946/139‑1 (MQ=255)

      aaaGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGTAAGGCCTATTAATCGCATTAACAGTTGCAGATAGAGtt                                                                                                                           <  1:156509/141‑1 (MQ=255)

          aagCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTa                                                                                                                       <  2:77961/141‑1 (MQ=255)

                         ttgcaATTCCAATGGCAATTAATTGAGTATCTTATTGTGAAAAAGAACCGATGGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAATGTTGCAGATAGAGTTGGTATTACTAGATCTGTaa                                                                                                        <  2:23828/140‑1 (MQ=255)

                         ctgctATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAATGTTGCAGATAGAGTTGGTATTACTAGATCTGTaa                                                                                                        <  1:120915/141‑1 (MQ=255)

                               ttAAAAAGGCAATTAATTCATTATCTTATTCTGACAAAGAAGTGATTGAACACATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTaa                                                                                                  <  1:189865/141‑1 (MQ=255)

                                 aCAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAATGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAAt                                                                                                >  1:213155/1‑141 (MQ=255)

                                 aCAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAAt                                                                                                <  1:264108/141‑1 (MQ=255)

                                     tGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAATGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCAc                                                                                            <  1:98205/141‑1 (MQ=255)

                                     tGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAATGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCAc                                                                                            <  1:98176/141‑1 (MQ=255)

                                      ggCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACt                                                                                           >  2:272307/1‑141 (MQ=255)

                                              attCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAATGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAAt                                                                                   >  2:260145/1‑141 (MQ=255)

                                                   ttttCTTAGTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAATGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGaa                                                                              <  2:121487/138‑1 (MQ=255)

                                                     aTCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAATGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAg                                                                            >  2:257773/1‑141 (MQ=255)

                                                             cTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGgtg                                                                    <  2:37923/141‑1 (MQ=255)

                                                                 aaaaGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAATGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAAt                                                                >  2:14038/1‑141 (MQ=255)

                                                                    agaagCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAATGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGa                                                             >  1:231866/1‑141 (MQ=255)

                                                                       agCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAATGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATc                                                          >  1:61225/1‑141 (MQ=255)

                                                                                  atatCTTTGAAGCACTTGGCGGTACGGAAGGCCGATTAATCGCATCAAATGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAg                                               <  2:157193/141‑1 (MQ=255)

                                                                                                cTTGGCGGTAAGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACt                                 <  1:252084/141‑1 (MQ=255)

                                                                                                   ggCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTc                              >  1:83811/1‑141 (MQ=255)

                                                                                                     cGGTCCGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGGATCACGTTCTTTAGGAATGAAAGGTACTTTCAt                            >  1:190730/1‑141 (MQ=255)

                                                                                                         aCGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTaaa                        <  2:181284/141‑1 (MQ=255)

                                                                                                          cGGAAGGCCTATTAATCGCATCAAATGTTGCAGATAGAGTTTGTATTACTAGATCTGTAATTGTAAATGCACTACGTAGATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAGTGAAAGGTACTTTCGTTAAAg                       >  1:212700/1‑141 (MQ=255)

                                                                                                          cGGAAGGCCTATTAATCGCATCAAATGTTGCAGATAGAGTTGGTATTACTAGATCTGTAGTTGTAAATGCACTACGTAAATTAGAAAGGGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTaaaa                       >  1:107871/1‑140 (MQ=255)

                                                                                                          cGGAAGGCCTATTAATCGCATCAAATGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTAAAg                       >  1:212709/1‑141 (MQ=255)

                                                                                                                       aaTCGCATCAAATGTTGCAGAAAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCTCGTTGTTTTGGAATGAAAGGTACTTTCATTAAAGTTAAAAAAGaaaa          >  1:145621/1‑141 (MQ=255)

                                                                                                                          cGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTAAAGTTAAAAAAGAAAAAtt       <  1:187663/141‑1 (MQ=255)

                                                                                                                               cAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTAAAGTTAAAAAAGAAAAATTCTTAg  <  1:144656/141‑1 (MQ=255)

GTAGAAAAAGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTAAAGTTAAAAAAGAAAAATTCTTAG  >  CP000730/1274081‑1274348

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