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
A9 F59 I0 R1	41	42.9	928050	95.2%	883503	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	76,969	G→A	100%	intergenic (+1027/‑107)	USA300HOU_0072 → / → USA300HOU_0075	universal stress protein/lysophospholipase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	76,969	0	G	A	100.0%	114.4 / NA	39	intergenic (+1027/‑107)	USA300HOU_0072/USA300HOU_0075	universal stress protein/lysophospholipase
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (26/13); total (26/13)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TCAGATCTACGGATTTTCGCCATGCCACGAAATTAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAGGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCATTATATAAAATTTATTGAGTCAAAA  >  CP000730/76834‑77105

tCAGATCTACGGATTTTCGCCATGCCACGAAATTAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAACACATGGGCTTAAAAGGTTa                                                                                                                                     >  2:367661/1‑141 (MQ=255)

       tACGGATTTTCGCCATGCCACGAGATTAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTtata                                                                                                                              >  2:83259/1‑141 (MQ=255)

               ttCGCCATGCCACGAAATTAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGAAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTa                                                                                                                      <  2:421932/141‑1 (MQ=255)

                tCGCCATGCCACGAAATTAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTAc                                                                                                                     >  1:33899/1‑141 (MQ=255)

                 cGCCATGCCACGAAATTAGCATCATGCTAGCAAATTTAGCGAACACTGCCATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACAAGGGCTTAAAAGGTTAATTTATATAGTAATACt                                                                                                                    >  1:221122/1‑141 (MQ=18)

                       gCCACGAAATTAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAAAATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAAc                                                                                                              >  2:245755/1‑141 (MQ=255)

                        ccACGAAATTAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACa                                                                                                             <  2:418907/141‑1 (MQ=255)

                           cGAAATTAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTTTAAAAAACATGGGCTTAAGAGGTTAGTTTATTTAGTTTTTCTGCAAACATTg                                                                                                          >  1:153097/1‑141 (MQ=17)

                                ttAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTGTTTTACTTTGCAACAGAACCTATATAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTg                                                                                                     <  1:298700/141‑1 (MQ=255)

                                 tAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGAGTTgg                                                                                                    >  1:123036/1‑141 (MQ=255)

                                   gCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGt                                                                                                  >  1:373479/1‑141 (MQ=255)

                                    gatcatGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTc                                                                                                 <  2:410911/140‑1 (MQ=255)

                                    catcatGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTc                                                                                                 >  1:282734/1‑141 (MQ=255)

                                           cTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAAtt                                                                                          >  2:455148/1‑141 (MQ=255)

                                              gCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACCGCAAACATTGATTTGGGTCAGAAATTAgg                                                                                       >  2:419138/1‑141 (MQ=255)

                                                 aGTTAAGCGAACACTGACATGATAAACTAGTGGTTAGCTATA‑TTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTa                                                                                   >  2:286744/1‑141 (MQ=255)

                                                  gTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTa                                                                                   <  1:72116/141‑1 (MQ=255)

                                                  gTTAAGCAAAAACTGACAAGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTa                                                                                   <  2:10067/141‑1 (MQ=255)

                                                   ttAAGCGAACACTGACATGATAAATTAGTGGTGAGCTATATTATTTAAAATAAAAAAAAAAAATAGAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGAAAACATTGATTTGGTTCaaaaaaaaaaaaaaa                                                                                  <  2:157867/141‑11 (MQ=19)

                                                     aaGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTGTAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTGCTGGAAACATTGATTTGGGTCAAACATAAGGTGTATTa                                                                                >  2:141561/1‑141 (MQ=25)

                                                              cTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTCGGGGTATTAAAAAaataa                                                                       >  2:215548/1‑139 (MQ=255)

                                                                      aTAAATTAGTGGTTAGCTATATTTTTTTAGTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCa                                                               >  1:246268/1‑141 (MQ=255)

                                                                         aaataatagtaagatatataTTTATACATTGCAACAGAACCTATAAAAAACATGGACTTAAAAGGTTAATTTATATAGTAGTACTGAAAACATTGATTTGTGTCAAAAATAAAAAAAAAAAAAAAAATGAATGAATCATaa                                                            <  2:411349/127‑1 (MQ=255)

                                                                         aaTTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATaa                                                            <  1:351266/141‑1 (MQ=255)

                                                                                ggTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATc                                                     >  1:135743/1‑141 (MQ=255)

                                                                                 gTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAATAGGTTAATTTATATAGTATTACTGCAAACATTGATTTCGGTCAAAAATTAGGGGTATTAAAAAAATAAAGGAATCATAATTTTATCa                                                    >  2:180710/1‑141 (MQ=39)

                                                                                 gTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAAGTTCATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAGAATGAATGAATCATAATTTTAtga                                                    >  2:199985/1‑139 (MQ=39)

                                                                                   tAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAg                                                  >  1:407699/1‑141 (MQ=255)

                                                                                       tataTTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGa                                              >  2:39508/1‑141 (MQ=255)

                                                                                           tttttttACTTTGCAACAGAACCTATAAAAAACATGGGCTTAGAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTCTCAAGCTGATTgg                                          >  1:157021/1‑141 (MQ=255)

                                                                                                 tACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGt                                    <  2:452867/141‑1 (MQ=255)

                                                                                                  aCTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGtt                                   >  1:420442/1‑141 (MQ=255)

                                                                                                                ccTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCATtatat                     >  1:130448/1‑141 (MQ=255)

                                                                                                                    taAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCATTATATaaaa                 >  1:241897/1‑141 (MQ=255)

                                                                                                                         aaCATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCATTATATAAAATTTAt            >  2:231526/1‑141 (MQ=255)

                                                                                                                               ggCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCATTATATAAAATTTATTGAGTc      <  2:373479/141‑1 (MQ=255)

                                                                                                                               ggCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCATTATATAAAATTTATTGAGTc      <  1:161759/141‑1 (MQ=255)

                                                                                                                                  ttAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCATTATATAAAATTTATTGAGTCaaa   >  2:296675/1‑141 (MQ=255)

                                                                                                                                   tAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCATTATATAAAATTTATTGAGTCaaaa  <  2:33899/141‑1 (MQ=255)

TCAGATCTACGGATTTTCGCCATGCCACGAAATTAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAGGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCATTATATAAAATTTATTGAGTCAAAA  >  CP000730/76834‑77105

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