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
A7 F123 I0 R1	46	52.8	1143652	95.1%	1087613	141.0

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%	142.5 / NA	47	intergenic (+1027/‑107)	USA300HOU_0072/USA300HOU_0075	universal stress protein/lysophospholipase
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (23/24); total (23/24)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CTTCAGATCTACGGATTTTCGCCATGCCACGAAATTAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAGGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCATTATATAAAATTTATTGAGTCAA  >  CP000730/76832‑77103

ctTCAGATCTACGGATTTTCGCCATGCCACGAAATTAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAGAAGGt                                                                                                                                     >  2:538506/1‑141 (MQ=255)

ctTCAGATCTACGGATTTTCGCCATGCCACGAAATTAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGGTAGCTATATTTTTTTACTTTGCAACAGAACCTATCAAAAACATGGGCGTAAAAGGt                                                                                                                                     >  1:57828/1‑141 (MQ=255)

  tCAGATCTACGGATTTTCGCCATGCCACGAAATTAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTa                                                                                                                                   <  1:146495/141‑1 (MQ=255)

     gATCTACGGATTTTCGCCATGCCACGAAATTAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAAtt                                                                                                                                >  1:4784/1‑141 (MQ=255)

     gATCTACGGATTTTCGCCATGCCACGAAATTAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAAtt                                                                                                                                >  2:270844/1‑141 (MQ=255)

       tCTACGGATTTTCGCCATGCCACGAAATTAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTta                                                                                                                              <  1:481252/141‑1 (MQ=255)

       tCTACGGATTTTCGCCATGCCACGAAATTAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAAAACCTATAAAAAACATGAGCTTAAAACTTTAAttaa                                                                                                                              >  2:24694/1‑139 (MQ=14)

        cTACGGATTTTCGCCATGCCACGAAATTAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTtat                                                                                                                             >  1:178231/1‑141 (MQ=255)

          aCGGATTTTCGCCATGCCACGAAATTAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATCTTTAAGTACTGTGCAACAGAACCTATAAAAAACATGGACTTAAAAGGTTAAGTtatat                                                                                                                           >  1:442386/1‑141 (MQ=17)

           cgtaTTTTCGCCATGCCACGAAATGAGCAACATGCTAGCAAGTTAAGCGAACACTCACAGTATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTtatata                                                                                                                          <  2:283982/138‑1 (MQ=17)

            ggATTTTCGCCATGCCCTGAAATTAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAg                                                                                                                         <  2:82947/141‑1 (MQ=255)

            ggATTTTCGCCATGCCACGAAATTAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAg                                                                                                                         <  2:210831/141‑1 (MQ=255)

               ttttCGCCATGCCACGAAATTAGCATCATGGTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTAt                                                                                                                      <  2:72212/141‑1 (MQ=255)

                tttCGCCATGCCACGAAATTAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTAtt                                                                                                                     <  1:241212/141‑1 (MQ=255)

                          ccACGAAATTAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACa                                                                                                           <  1:239672/141‑1 (MQ=255)

                                     gCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAACCATTGATTTgggg                                                                                                >  2:332188/1‑140 (MQ=255)

                                      aatcatGCTAGCAAGCTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTc                                                                                               <  1:118103/140‑1 (MQ=255)

                                             cTAGCAAGTTAAGCGAACACTGACATGATGAATTAGTGGTTAGCTATATTTTTTTTTTTTTTATCAGAACCTATAAAAAAAATGGGCTTTAAAAGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAAtt                                                                                        >  2:371548/1‑141 (MQ=25)

                                                       aaacaaaCACTGACATGAAAAAAAACTAGTAAGCTAAATTTTATTATTGAGCAAAAAAAAAAAAAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTa                                                                              <  2:428182/136‑1 (MQ=255)

                                                       aaGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTAGGGTCAAAAATTAGGGGTATTa                                                                              >  1:332569/1‑141 (MQ=255)

                                                         gCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAAAATATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAACAATAGATTTGGGTCAAAAATTAGGGGTATTaaa                                                                            >  2:187612/1‑141 (MQ=37)

                                                                cTGACATGATAAATTCGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAaatga                                                                     >  1:423758/1‑141 (MQ=255)

                                                                    cATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCACAAATTAGGGGTATTAAAAAAatgaatga                                                                 >  1:309001/1‑141 (MQ=255)

                                                                       gATAAATTAGTGGTTATCTATACTTTTTTCCTTTGCAACAGAACCGATCAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTACTGGTATGAAAAAAATGAATGAATc                                                              <  1:278010/141‑1 (MQ=255)

                                                                         tAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCAt                                                            <  1:139415/141‑1 (MQ=255)

                                                                            aTTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAAt                                                         >  1:103407/1‑141 (MQ=255)

                                                                               aGTGGATAGCTATATTTTTTTCCTTTTCAATAGAACCTATAAAAAACATGGGGTGAAAAGGTTATCTTAAATAGTGGTACTGCAAACATTGATCGGGTTCAAAAATTAGAAAAAAAAAAAAAATGAATGAATCATAAtttt                                                      <  2:392973/141‑1 (MQ=255)

                                                                                gTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACCTGGGCTTCAAAGTTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAACTTAGGGGTATTAAAAAAAAGAATCAATCATAATTTTa                                                     >  2:271814/1‑141 (MQ=38)

                                                                                  ggTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATc                                                   >  1:230644/1‑141 (MQ=255)

                                                                                               tttttACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGgag                                      >  1:534824/1‑141 (MQ=255)

                                                                                                  ttACGTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAgg                                   <  2:421990/141‑1 (MQ=255)

                                                                                                   tACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGt                                  <  2:423758/141‑1 (MQ=255)

                                                                                                        tGCAACAGAACCTATAAAACCAATAAGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATACTTTTATGCAGCTGATTGGAGAGGTTaaaa                             >  2:123509/1‑141 (MQ=255)

                                                                                                        tGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAAGGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTaaaa                             >  2:379494/1‑141 (MQ=255)

                                                                                                        tGCAACAGAACCTATAAAAAACACGGGCTTAAAAGGTTACTTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGCTTacaa                             >  2:33897/1‑141 (MQ=255)

                                                                                                             acaaaCATAAAAAAAACATGGTCTTAAAAGGTTAATGTACAAAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGCATTAAAAAAATGAATGAATCATAATTTTCTCAAGCTGATTGGAGAGGTTAAAATGCAt                        <  2:5477/138‑1 (MQ=255)

                                                                                                             aaGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCAt                        <  2:545942/140‑1 (MQ=255)

                                                                                                              aGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAAAGCAtt                       >  2:473766/1‑141 (MQ=255)

                                                                                                                   cTATAAAAAACATGGGCTTAACACACTTATTGATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCATtatcta                  >  2:549686/1‑141 (MQ=255)

                                                                                                                   cTATAAAAAACATGGGCTTAAAACGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATTATTTTATCAAGCTGATTGGAGAGGTTAAAATGCATtatata                  <  2:242234/141‑1 (MQ=255)

                                                                                                                     ataAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCATTATATaaa                <  1:567255/141‑1 (MQ=255)

                                                                                                                     ataAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCATTATATaaa                >  1:560484/1‑141 (MQ=255)

                                                                                                                     ataAAAAACAAGGGCTTAAAAGGTTAATTTATATAGTATTACAACAAACATTGATTTGGGTCAAAAATAAAAAAAAAAAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCATTATATaaa                <  2:114458/141‑1 (MQ=255)

                                                                                                                              aTGGGTTTAAAAGGTTAATTTATATAATAATACCGCAAACATTGATTTGGGTC‑AAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCATTATATAAAATTTATTGAg      <  2:252429/141‑1 (MQ=255)

                                                                                                                               tGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCATTATATAAAATTTATTGAg      <  1:42396/141‑1 (MQ=255)

                                                                                                                                  gCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCATTATATAAAATTTATTGAGTCa   <  1:354941/141‑1 (MQ=255)

                                                                                                                                   cTTAAAAGGTTAATTTATATAGTATTACTGCAAACAGTGATTTTGGTCAAAAAATACAGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCATTATATAAAATTTATTGAGTCaa  <  2:332569/141‑1 (MQ=255)

CTTCAGATCTACGGATTTTCGCCATGCCACGAAATTAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAGGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCATTATATAAAATTTATTGAGTCAA  >  CP000730/76832‑77103

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