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
A5 F58 I0 R1	46	56.2	1222162	96.0%	1173275	141.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	76,969	G→A	21.3%	intergenic (+509/‑107)	USA300HOU_RS00140 → / → USA300HOU_RS00350	hypothetical protein/Monoacylglycerol lipase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	76,969	0	G	A	21.3%	64.9 / 8.4	36	intergenic (+509/‑107)	USA300HOU_RS00140/USA300HOU_RS00350	hypothetical protein/Monoacylglycerol lipase
Reads supporting (aligned to +/- strand): ref base G (12/16); new base A (3/5); total (15/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TCTTCAGATCTACGGATTTTCGCCATGCCACGAAATTAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAGGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCATTATATAAAATTTATTGAGTCAAAAGAT  >  USA300TCH1516_ALE/76831‑77108

tctTCAGATCTACGGATTTTCGCCATGCCACGAAATTAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAGAggg                                                                                                                                           >  1:559514/1‑141 (MQ=255)

    cAGATCTACGGATTTTCGCCATGCCACGAAATTAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACATTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTaa                                                                                                                                       <  1:190628/141‑1 (MQ=255)

           aCGGATTTTCGCCATGCCACGAAATTAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAGGGTTAATTtatat                                                                                                                                <  1:151400/141‑1 (MQ=255)

             ggATATTCGACAGGCCCAGAAAGTGGCATTATGCTAGCAAGTTAAGCGAACCCTGAGATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCGAGAAAAAACACGGGCTTAAAGGGCTAATTTATATAg                                                                                                                              <  2:103654/141‑1 (MQ=17)

                 tttCGCCATGCCACGAAATTAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATTAATTAGTGGTTAGCTATATTTTTTTTCTTTGTATAGGTACCTATAAAAAAAATGGGTTTAAAAGGTTAATTTTTATTGTAtt                                                                                                                          >  2:546353/1‑141 (MQ=14)

                  ttCGCCATGCCACGAAATTAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTCTGCAACAGAACCTATAAAAAACATGGGCTTAAAGGGTTAATTTATATAGTATTa                                                                                                                         <  1:395267/141‑1 (MQ=255)

                   tCGCCATGCCACGAAATTAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCGACATAACCTATAAAAAACATGGGCTTAAAAGGGTAATTTATAGAGTATTAc                                                                                                                        >  1:277180/1‑141 (MQ=18)

                   tCGCCATGCCACGAAATTAGCATCATGATAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTAc                                                                                                                        <  2:357851/141‑1 (MQ=255)

                        aTGCCACGAAATTAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAGGGTTAATTTATATAGTATTACTGCaa                                                                                                                   <  1:90359/141‑1 (MQ=255)

                                       catcatGCTAGCAAGTTAAGCGAAAACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAGGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTc                                                                                                    >  2:576743/1‑141 (MQ=255)

                                        atcatGCTTGCAATGTAAGCTATCACTGACAGGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCGATAAAAAACATGGGCTTAAAGGGTTAATTTATACAGTATTACTGCAAACATTGATTTGGGTCa                                                                                                   <  2:591401/141‑1 (MQ=25)

                                           atGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCGATAAAAAACATGGGCTTAAAGGGTTAATTTATATAGTATTACTGTAAAAATTGATGTGGGTCacaa                                                                                                >  1:51053/1‑141 (MQ=21)

                                                 gCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTAAAAGGGTTAATTTATGTAGTATTACGGCAAACATTGATTTGGCTCAAAAAttttg                                                                                          >  2:237492/1‑138 (MQ=25)

                                                         aGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACATATAAAAAACATGGGCTTAAAGGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGGATTaa                                                                                  >  2:205463/1‑141 (MQ=255)

                                                          gCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAGGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTaaa                                                                                 >  1:38983/1‑141 (MQ=255)

                                                                  tGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAaatgaa                                                                         <  1:418317/141‑1 (MQ=255)

                                                                             aTTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAGGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAAt                                                              >  1:284636/1‑141 (MQ=255)

                                                                               tAGTGGTTAGCTATATTTTTTTTTTTTTTTACAGAACCTATAAAAAGCATGGGCTTAAAGGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAAttt                                                            >  2:390255/1‑141 (MQ=255)

                                                                                  tGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAGGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGCGTATTAAACAGATGATTGAATCATCATTTTAt                                                         >  1:260211/1‑141 (MQ=39)

                                                                                      tAGCTATATTTTTTTACGTTGCAACAGAACCTATAAAAAACATGGGCTTAAAGGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAg                                                     <  2:494597/141‑1 (MQ=255)

                                                                                         cTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAGGGTTCCCCGATTTATTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTg                                                  <  1:444045/141‑1 (MQ=255)

                                                                                         cTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAGGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTg                                                  <  2:511925/141‑1 (MQ=255)

                                                                                           atatTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAGGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCAGAt                                                >  2:515162/1‑141 (MQ=255)

                                                                                            tatTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGAtt                                               >  1:561860/1‑141 (MQ=255)

                                                                                             atTTTTTTACTTTGCAACAGGACCTATAAAAAACATGGGCTTAAAGGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTg                                              <  2:459985/141‑1 (MQ=255)

                                                                                                tttttACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAGGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGgag                                           <  1:284656/141‑1 (MQ=255)

                                                                                                       attGCAAGAACACCTAAAAAAAACACGAGATTAAAGGGTTAAATTATATTGTATTACTGCAAACATAAAAAAAAAAAAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAATCTGATTGGAGAGGTTaa                                    <  2:190801/140‑1 (MQ=255)

                                                                                                           aaaCAGAACAAATGAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATg                                <  2:7923/140‑1 (MQ=255)

                                                                                                                gAACCTATAAAAAACATGGGCTTAAAGGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCATta                           >  1:193800/1‑141 (MQ=255)

                                                                                                                      ataAAAAACAAGGGCTTAAAGGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAAGGCTATTCAAACAATTAACCAATCATAATTTTCTCCAGCCTATTGGAGAGGTTAAAATGCATTATATaaa                     <  2:585250/141‑1 (MQ=255)

                                                                                                                         taaaaaaTGGGACTAAAGGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCATTATATAAAAtt                  <  1:429021/140‑1 (MQ=255)

                                                                                                                             aCATGGGCTTAAAAGGATAATTCAAATAGTATTACTGCAAACATTGATTTGAGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCATTATATAAAATTTAtt              <  1:546353/141‑1 (MQ=255)

                                                                                                                              cATGGGCTTAAAGGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCATTATATAAAATTTATTg             >  1:207877/1‑141 (MQ=255)

                                                                                                                                 gggCTTAAAGGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCATTATATAAAATTTATTGAGt          <  2:10827/141‑1 (MQ=255)

                                                                                                                                 gggCTGAATGAGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATGAGGGGTATTAAAAAAATGAATGAATCACAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCATTATATAAAATTTATTGAGt          <  2:51053/141‑1 (MQ=255)

                                                                                                                                    cTTAAAGGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCATTATATAAAAtttttttatccat       <  2:527461/141‑8 (MQ=255)

                                                                                                                                         aGGGTTAATTTATATAGTATTAATGAAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCGGATTGAAGAGGTTAAAATGCATTATATAAAATTTATTGAGTCAAAAGat  >  2:290407/1‑141 (MQ=255)

TCTTCAGATCTACGGATTTTCGCCATGCCACGAAATTAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAGGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCATTATATAAAATTTATTGAGTCAAAAGAT  >  USA300TCH1516_ALE/76831‑77108

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