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 F184 I0 R1	45	69.8	1527574	94.8%	1448140	140.0

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%	100.5 / NA	36	intergenic (+1027/‑107)	USA300HOU_0072/USA300HOU_0075	universal stress protein/lysophospholipase
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (16/20); total (16/20)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TTCAGATCTACGGATTTTCGCCATGCCACGAAATTAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATA‑TTTTTTTACTTTGCAACAGAACCT‑ATAAAAAACATGGGCTTAAAGGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCATTATATAAAATTTATTGAGTC  >  CP000730/76833‑77101

ttCAGATCTACGGATTTTCGCCATGCCACGAAATTAGCATCATGCTAGAAAGTTAAACGAACACTGACATGATAAATTAGTGGTTAGCTATA‑TTTTTTTACTTTGCAACAGAACCT‑ATAAAAAACATGGGCTTAAAAGGt                                                                                                                                   <  1:518333/140‑1 (MQ=255)

   aGATCTACGGATTTTCGCCATGCCACGAAATTAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATA‑TTTTTTTACTTTGCAACAGAACCT‑ATAAAAAACATGGGCTTAAAAGGTTaa                                                                                                                                <  1:718578/140‑1 (MQ=255)

    gATCTACGGATTTTCGCCATGCCACGAAATTAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATA‑TTTTTTTACTTTGCAACAGAACCT‑ATAAAAAACATGGGCTTAAAAGGTTAAt                                                                                                                               >  1:693019/1‑140 (MQ=255)

     ctCTAGGGATTTTCGCCATGCTACGAAATTCGCATTATGCTAGCAAGTGAAGCGAACACTGCGATGATAAATTAGTGGTTAGCTACATTTTTTTTACTTTGCAACAGAACCT‑ATAATAAACATGGGCTTAAAAGGTTAAt                                                                                                                               <  2:192672/139‑1 (MQ=14)

      tcaaCGGAGTTTAGACATGCCACGAAATTAGCATCATGCTAGCAAGTTAAGCGAACACCGACATGATAAATAAGTGGTTAGCTATA‑TTTTTTTACTTTGCAAAAAAAAAA‑AAAAAAAACATGGGCTTAAAAGGTTAAttt                                                                                                                             <  2:504047/137‑1 (MQ=14)

         aCGGATTTTCGCCATGCCACGAAATTAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATA‑TTTTTTTACTTTGCAACAGAACCT‑ATAAAAAACATGGGCTTAAAAGGTTAATTtata                                                                                                                          <  1:427922/140‑1 (MQ=255)

            gATTTTCGCCATGCCACGAAATTAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATA‑TTTTTTTACTTTGCAACAGAACCT‑ATAAAAAACATGGGCTTAAAAGGTTAATTTATATAg                                                                                                                       >  2:546235/1‑140 (MQ=255)

                    ccacgccacgAAATTAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATA‑TTTTTTTACTTTGCAAAAAAAAAA‑AAAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTg                                                                                                               <  2:467634/140‑1 (MQ=17)

                                aTTAGCATCATTCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATA‑TTTTTTTACTTTGCAACAGAACCT‑ATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGAtt                                                                                                   <  1:753568/140‑1 (MQ=255)

                                   aGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATA‑TTTTTTTACTTTGCAACAGCACCT‑ATAAAATACATGGTGGTATAAGGTTTATTTATATAGAGTTAGTGCAAACTTTGATTTgg                                                                                                >  1:669961/1‑140 (MQ=17)

                                   aGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATA‑TTTTTTTACTTTGCAACAGAACCT‑ATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTgg                                                                                                <  2:693019/140‑1 (MQ=255)

                                   aGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATA‑TTTTTTTACTTTGCAACAGAACCT‑ATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTgg                                                                                                >  1:482603/1‑140 (MQ=255)

                                            cTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATA‑TTTTTTTACTTTGCAACAGAACCT‑ATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAAt                                                                                       <  1:230767/140‑1 (MQ=255)

                                               gCAAGTTAAGCGAACACTGAGATGATAAATTAGTGGTTAGCTATA‑TTTTTTTACTTTGGAACAGAACCT‑ATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCTAACATTGATTCGGGTCAAAAATTAg                                                                                    >  1:460922/1‑140 (MQ=25)

                                               gCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATA‑TTTTTTTACTTTGCAACAGAACCT‑ATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAg                                                                                    >  1:680801/1‑140 (MQ=255)

                                                     tAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATA‑TTTTTTTACTTTGCAACAGAACCT‑ATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTAt                                                                              <  2:39894/140‑1 (MQ=255)

                                                      aaGCGAACACTGACATGATAAATTAGTGGTTAGCTATA‑TTTTTTTACTTTGCAACAGAACCT‑ATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTAtt                                                                             <  1:51848/140‑1 (MQ=255)

                                                       aGCGAACACTGACATGATAAATTAGTGGTTAGCTATA‑TTTTTTTACTTTGCAACAGAACCT‑ATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTa                                                                            <  1:219066/140‑1 (MQ=255)

                                                       aGCGAACACTGACATGATAAATTAGTGGTTAGCTATA‑TTTTTTTACTTTGCAACAGAACCT‑ATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTa                                                                            <  1:6040/140‑1 (MQ=255)

                                                             cacTGACATGATAAATTAGTGGTTAGCTATA‑TTTTTTTACTTTGCAACAGAACCT‑ATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTaaaaaaa                                                                      >  2:331986/1‑140 (MQ=255)

                                                                       aTAAAATACTGGTAAGCTATA‑TTTTTTTACTTTGCCACTGATCAT‑ATGAAAAACATGGCATTAAAAGCTTAATTGCTATAGTATTACTGCATACATTGATTTGGGTCGAACAATATGGGCATTAAAAAAATgaatgtata                                                            >  2:37230/1‑139 (MQ=255)

                                                                        tAAATTAGTGGTTAGCTATA‑TTTTTTTACTTTGCAACAGAACCT‑ATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAAGgaatgaataa                                                           >  2:707420/1‑138 (MQ=255)

                                                                                       cTATA‑TTTTTTTACTTTGCAACAGAACCT‑ATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCt                                            >  1:73988/1‑140 (MQ=255)

                                                                                       cTATA‑TTTTTTTACTTTGCAACAGAACCT‑ATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCt                                            >  2:583209/1‑140 (MQ=255)

                                                                                          ta‑tTTTTTTACTTTGCAACAGAACCT‑ATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTTATTTGGGTCAAAAATTAGGGGTATTAAAAAAATTAATGAATCATAATTTTATCAAGCTGAt                                         <  2:96338/140‑1 (MQ=255)

                                                                                                  ttACTTTGCAACAGAACCT‑ATAAAAAACATGGTCTTAAAAGGTTAATTTATATTGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGagag                                  <  1:613770/140‑1 (MQ=255)

                                                                                                  ttACTTTGCAACAGAACCT‑ATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGagag                                  >  1:612014/1‑140 (MQ=255)

                                                                                                  ttACTTTGCAACAGAACCT‑ATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGagag                                  <  1:502409/140‑1 (MQ=255)

                                                                                                   taacttGCAAAAAAACCTAAAAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCGAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGagag                                  <  1:690070/136‑1 (MQ=255)

                                                                                                       ttGCAACAGAACCT‑ATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTaa                             <  1:81770/140‑1 (MQ=255)

                                                                                                       ttGCAACAGAACCT‑ATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGAATGGAGAGGTTaa                             >  1:209478/1‑140 (MQ=255)

                                                                                                             cAGAACCT‑ATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCa                       >  1:55419/1‑140 (MQ=255)

                                                                                                                    t‑ataAAAAACATGGGTTTAACAGGTTAATTTATATTGTCTTCCTCCTTTTACACATTTGGGTCAAAAATTAGGTGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCATtatata                <  1:171544/140‑1 (MQ=255)

                                                                                                                        aaaaaaCATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGAATTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCATTATATaaaa             >  1:401467/1‑140 (MQ=255)

                                                                                                                        aaaaaaCATGGGCTTAAAAGGTTAATATATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGACAGGTTAAAATGCATTATATaaaa             >  2:348437/1‑140 (MQ=255)

                                                                                                                                   gCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTTAAAAATTAGGGGTATTAAAAAAATGAATTAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCATTATATAAAATTTATTGAGTc  <  2:259502/140‑1 (MQ=255)

TTCAGATCTACGGATTTTCGCCATGCCACGAAATTAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATA‑TTTTTTTACTTTGCAACAGAACCT‑ATAAAAAACATGGGCTTAAAGGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCATTATATAAAATTTATTGAGTC  >  CP000730/76833‑77101

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A