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 I1 R1	34	38.2	765948	97.1%	743735	148.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP000730	2,035,886	T→C	intergenic (‑212/‑3)	USA300HOU_1892 ← / → dnaQ	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	100.0%	113.9 / NA	30	intergenic (‑212/‑3)	USA300HOU_1892/dnaQ	hypothetical protein/DNA‑directed DNA polymerase III
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (17/13); total (17/13)

ATATCATCATTTACTTTTTAATCAGAGTTACATCCAAATGATAGATTTCACGTTATACCTTCACGTATAATATTATGTATCGTTTGTAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACTACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTCTGTCGGAATGGTTAAAGTCATTGATAGTCAAATAACAGAAACATTTCATACTCTTGTGAATCCGCAAGAC  >  CP000730/2035743‑2036026

atatCATCATTTACTTTTTAATCAGAGTTACATCCAAATGATAGATTTCACGTTATACCTTCACGTATAATATTATGTATCGTTTGTAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACCACAt                                                                                                                                          <  1:106764/148‑1 (MQ=255)

atatCATCATTTACTTTTTAATCAGAGTTACATCCAAATGATAGATTTCACGTTATACCTTCACGTATAATATTATGTATCGTTTGTAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACCACAt                                                                                                                                          <  2:23835/148‑1 (MQ=255)

     atcatTTACTTTTTAATCAGAGTTACATCCAAATGATAGATTTCACGTTATACCTTCACGTATAATATTATGTATCGTTTGTAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACCACATGATAc                                                                                                                                     <  1:314915/148‑1 (MQ=255)

        atTTACTTTTTAATCAGAGTTACATCCAAATGATAGATTTCACGTTATACCTTCACGTATAATATTATGTATCGTTTGTAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACCACATGATACAAg                                                                                                                                  >  2:103414/1‑148 (MQ=255)

        atTTACTTTTTAATCAGAGTTACATCCAAATGATAGATTTCACGTTATACCTTCACGTATAATATTATGTATCGTTTGTAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACCACATGATACAAg                                                                                                                                  >  2:152475/1‑148 (MQ=255)

                     tCAGAGTTACATCCAAATGATAGATTTCACGTTATACCTTCACGTATAATATTATGTATCGTTTGTAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGc                                                                                                                     <  1:228480/148‑1 (MQ=255)

                           ttACATCCAAATGATAGATTTCACGTTATACCTTCACGTATAATATTATGTATCGTTTGTAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGa                                                                                                               <  1:10813/148‑1 (MQ=255)

                                 ccAAATGATAGATTTCACGTTATACCTTCACGTATAATATTATGTATCGTTTGTAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGa                                                                                                         <  2:45432/148‑1 (MQ=255)

                                         tAGATTTCACGTTATACCTTCACGTATAATATTATGTATCGTTTGTAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCaa                                                                                                 >  1:127402/1‑148 (MQ=255)

                                               tCACGTTATACCTTCACGTATAATATTATGTATCGTTTGTAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGTTTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTa                                                                                           >  1:290390/1‑148 (MQ=255)

                                               tCACGTTATACCTTCACGTATAATATTATGTATCGTTTGTAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTa                                                                                           <  2:174315/148‑1 (MQ=255)

                                               tCACGTTATACCTTCACGTATAATATTATGTATCGTTTGTAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTa                                                                                           <  2:42949/148‑1 (MQ=255)

                                               tCACGTTATACCTTCACGTATAATATTATGTATCGTTTGTAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTa                                                                                           <  2:42970/148‑1 (MQ=255)

                                               tCACGTTATACCTTCACGTATAATATTATGTATCGTTTGTAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTa                                                                                           >  2:179083/1‑148 (MQ=255)

                                                          cTTCACGTATAATATTATGTATCGTTTGTAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGt                                                                                >  1:86254/1‑148 (MQ=255)

                                                          cTTCACGTATAATATTATGTATCGTTTGTAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGt                                                                                >  1:86769/1‑148 (MQ=255)

                                                                  ataataTTATGTATCGTTTGTAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTc                                                                        >  1:89970/1‑148 (MQ=255)

                                                                  ataataTTATGTATCGTTTGTAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTc                                                                        >  1:376804/1‑148 (MQ=255)

                                                                              aTCGTTTGTAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTCTGTCGGAATGGt                                                            >  1:271497/1‑148 (MQ=255)

                                                                                       aaGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTCTGTCGGAATGGTTAAAGTCAt                                                   <  2:334340/148‑1 (MQ=255)

                                                                                          cAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTCTGTCGGAATGGTTAAAGTCATTGa                                                >  2:265258/1‑148 (MQ=255)

                                                                                           aaaTGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTCTGTCGGAATGGTTAAAGTCATTGAt                                               >  2:120606/1‑148 (MQ=255)

                                                                                                            ttAATATATACATTTAATTAATTGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTCTGTCGGAATGGTTAAAGTCATTGATAGTCAAATAACAGAAAc                              <  2:65524/148‑1 (MQ=255)

                                                                                                               atatatACATTTAATTAATTGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTCTGTCGGAATGGTTAAAGTCATTGATAGTCAAATAACAGAAACAtt                           <  1:230762/148‑1 (MQ=255)

                                                                                                                      cATTTAATTAATTGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTCTGTCGGAATGGTTAAAGTCATTGATAGTCAAATAACAGAAACATTTCATAct                    >  1:150309/1‑148 (MQ=255)

                                                                                                                               aattGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTCTGTCGGAATGGTTAAAGTCATTGATAGTCAAATAACAGAAACATTTCATACTCTTGTGAAt           >  2:18699/1‑148 (MQ=255)

                                                                                                                                 ttGAAAGGATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTCTGTCGGAATGGTTAAAGTCATTGATAGTCAAATAACAGAAACATTTCATACTCTTGTGAATcc         <  2:310058/148‑1 (MQ=255)

                                                                                                                                       ggATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTCTGTCGGAATGGTTAAAGTCATTGATAGTCAAATAACAGAAACATTTCATACTCTTGTGAATCCGCAAGa   >  1:31138/1‑148 (MQ=255)

                                                                                                                                        gATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTCTGTCGGAATGGTTAAAGTCATTGATAGTCAAATAACAGAAACATTTCATACTCTTGTGAATCCGCAAGAc  >  1:107491/1‑148 (MQ=255)

                                                                                                                                        gATTGACCACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTCTGTCGGAATGGTTAAAGTCATTGATAGTCAAATAACAGAAACATTTCATACTCTTGTGAATCCGCAAGAc  >  1:190700/1‑148 (MQ=255)

ATATCATCATTTACTTTTTAATCAGAGTTACATCCAAATGATAGATTTCACGTTATACCTTCACGTATAATATTATGTATCGTTTGTAAGCAAATGACTAAAAGTCTATTAATATATACATTTAATTAATTGAAAGGATTGACTACATGATACAAGATGCGTTTGTTGCACTTGATTTTGAAACAGCAAATGGTAAACGTACAAGTATTTGTTCTGTCGGAATGGTTAAAGTCATTGATAGTCAAATAACAGAAACATTTCATACTCTTGTGAATCCGCAAGAC  >  CP000730/2035743‑2036026

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A