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	2,035,886	T→C	66.2%	intergenic (‑212/‑3)	USA300HOU_1892 ← / → USA300HOU_1893	hypothetical protein/DNA‑directed DNA polymerase III

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,035,886	0	T	C	66.2%	21.7 / 12.5	24	intergenic (‑212/‑3)	USA300HOU_1892/USA300HOU_1893	hypothetical protein/DNA‑directed DNA polymerase III
Reads supporting (aligned to +/- strand): ref base T (3/5); new base C (12/3); total (16/8)
Fisher's exact test for biased strand distribution p-value = 7.13e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

TCATCATTTACTTTTTAATCAGAGTTACATCCAAATGATAGATTTCACGTTATACCTTCACGTATAATATTATGTATCGTTTGTAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACTACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTCTGTCGGAATGGTTAAAGTCATTGATAGTCAAATAACAGAAACATTTCATACTCTTGTGAATCCGCAA  >  CP000730/2035746‑2036023

tcatcaTTTACTTTTTAATCAGAGTTACATCCAAATGATAGATTTCACGTTATACCTTCACGTATAATATTATGTATCGTTTGTAAGCAAACGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGCTTTACt                                                                                                                                           >  2:82591/1‑141 (MQ=255)

     atTTACTTTTTAATCAGAGTTACATCCAAATGATGGATTTCACGTTATACCTTCACGTATAATATTATGTATCGTTTATAAGCAAATGACTAAAAGTATATTAATATATACATTTAATTAATTGCAAGGATTTACCACATg                                                                                                                                      >  2:84314/1‑141 (MQ=255)

          cTTTTTAATCAGAGTTACATCCAAATGATAGATTTCACGTTATACCTTCACGTATAATATTATGTATCGTTTGTAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTAAAATGATTGACAACATGATACa                                                                                                                                 >  1:84095/1‑141 (MQ=255)

                                        gATTTCACGTTATACCATCACGTATAATACTATGACTCGAGTGATAGCAAATGACTAAGAGTCTATTAATATATACATTTAACTAATTGAAAGGATTGTCTACCTGATACAAGATGCGTTTGTGGCACTTGATATTGAGAc                                                                                                   >  2:127866/1‑141 (MQ=255)

                                             aaatatataCCTTGAATAATAATATGATGTATGGTTTGTAAGGATATGTCTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACTAAATGATACAAGATGCGTTTGTTGCACTAGATTTTGAAACAGCaa                                                                                              <  1:51274/136‑1 (MQ=255)

                                                            cGTATAATATTATGTATCGTTTGTAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACTACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACaa                                                                               <  2:159855/141‑1 (MQ=255)

                                                             gTATAATATTATGTATCGTTTGTAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACCACATGATACTAGACGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAg                                                                              <  1:192438/141‑1 (MQ=255)

                                                                  atatTATGTATCGTTTGTAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTAttt                                                                         >  2:254382/1‑141 (MQ=255)

                                                                             cGTTTGTAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACTACATGATACAAGATGCGTTTGTTGCATTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTCTGTCGGa                                                              <  2:206353/141‑1 (MQ=255)

                                                                                   tAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTCTGTCGGAATGGtt                                                        >  1:44740/1‑141 (MQ=255)

                                                                                   tAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTCTGTCGGAATGGtt                                                        >  1:233780/1‑141 (MQ=255)

                                                                                         aaTGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTCTTTCGGAATGGATAAAGTc                                                  >  2:191992/1‑141 (MQ=255)

                                                                                            gACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTCTGTCGGAATGGTTAAAGTCAtt                                               >  1:225149/1‑141 (MQ=255)

                                                                                              cTAAAAGTCTATTACTATATACATTTCATTAATTGAAAGGATTGACTACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACCGCTAATGTTAAACGTACAAGTATTTGTTCTGTCGGAATGGTTAAAGTCATTGa                                             <  1:162539/141‑1 (MQ=255)

                                                                                                       tATTAATATATACATTTAATTAATTGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTCTGTCGGAATGGTTAAAGTCATTGATAGTCAAAt                                    >  1:275861/1‑141 (MQ=255)

                                                                                                        aTTAATATATACATTTAATTAATTGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAAGGGTAAACGTACAAGTATTTGTTCTGTCGGAATGGTTAAAGTCATTGATAGTCAAATa                                   >  2:120003/1‑141 (MQ=255)

                                                                                                                ataCATTTAATTAATTGAAAGGATTGACCACATGATACAAGATACGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTCTGTCGGACTGGCTACAGTCAATGATAGTACAATAACAGaaaa                           >  1:26839/1‑140 (MQ=255)

                                                                                                                     tttAATTAATTGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCACATGGTAAACGTACAAGTATTTGTCCTGTCGGAATGGTTAAAGTCATTGTTAGTCAAATAACAAAACCAGTTc                      >  2:41759/1‑141 (MQ=255)

                                                                                                                     tttAATTAATTGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTCTGTCGGAATGGTTAAAGTCATTGATAGTCAAATAACAGAAACATTTc                      <  1:254382/141‑1 (MQ=255)

                                                                                                                         attaattGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACaa                                                                               <  1:77535/80‑1 (MQ=255)

                                                                                                                         attaattGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACaa                                                                               >  2:77535/1‑80 (MQ=255)

                                                                                                                              ttGAAAGGATTGACTACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTCTGTCGGAATGGTTAAAGTCATTGATAGTCAAATAACAGAAACATTTCATACTCTtg             <  1:117921/141‑1 (MQ=255)

                                                                                                                                        tGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTCTGTCGGAATGGTTAAAGTCATTGATAGTCAAATAACAGAAACATTTCATACTCTTGTGAATCCGCa   >  1:191751/1‑141 (MQ=255)

                                                                                                                                         gACTACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTCTGTCGGAATGGTTAAAGTCATTGATAGTCAAATAACAGAAACATTTCATACTCTTGTGAATCCGCaa  >  1:257778/1‑141 (MQ=255)

                                                                                                                                         gACTACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTCTGTCGGAATGGTTAAAGTCATTGATAGTCAAATAACAGAAACATTTCATACTCTTGTGAACCCGCaa  >  2:76687/1‑141 (MQ=255)

TCATCATTTACTTTTTAATCAGAGTTACATCCAAATGATAGATTTCACGTTATACCTTCACGTATAATATTATGTATCGTTTGTAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACTACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTCTGTCGGAATGGTTAAAGTCATTGATAGTCAAATAACAGAAACATTTCATACTCTTGTGAATCCGCAA  >  CP000730/2035746‑2036023

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