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
A1 F169 I0 R1	132	34.5	794130	89.8%	713128	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	51,327:1	+G	100%	coding (29/1092 nt)	USA300HOU_0043 →	hypothetical membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	51,327	1	.	G	53.8%	34.3 / 45.7	26	coding (29/1092 nt)	USA300HOU_0043	hypothetical membrane protein
Reads supporting (aligned to +/- strand): ref base . (5/7); new base G (7/7); total (12/14)
Fisher's exact test for biased strand distribution p-value = 7.13e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.68e-01
Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch.

ATTTCTTATTCATTTTAAAATTCCTCCAATAATTTTTAAGGAGTCAATCAATATCATATAGGTTAAACTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGG‑A‑GGG‑GGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGTAACAGTTGAGGTTTATGAAGATTTGTTGTTATTAAGAAGTTTAAG  >  CP000730/51190‑51453

aTTTCTTATTCATTTTAAAATTCCTCCAATAATTTTTAAGGAGTCAATCAATATCATATAGGTTAAACTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGG‑A‑ggg                                                                                                                              >  1:371795/1‑141 (MQ=255)

aTTTCTGATTCATTTTAAAATTCCGCCAATAATATTTAAGGAGTCAATCAATATCATATAGGTTTAACTATCTTCAATGGATTGCTATAATAAGCATAGATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGG‑A‑ggg                                                                                                                              <  2:181645/141‑1 (MQ=255)

    cTTATTCATTTTAAAATTCCTCCAATAATTTTTAAGGAGTCAATCAATATCATATAGGTTAAACTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGG‑A‑ggg‑gggg                                                                                                                         >  1:69770/1‑141 (MQ=255)

    cTTATTCATTTTAAAATTCCTCCAATAATTTTTAAGGAGTCAATCAATATCATATAGGTTAAACTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATGAGACGCGGAACAAAAAATGGGG‑A‑ggg‑gggg                                                                                                                         >  2:251156/1‑141 (MQ=255)

           aTTTTAAACTTCATCCTATAAGTTTAAAGGAGGCAATCAATATCAAATAGGTTAAACTATCTTCAATTGATTGCTATATCAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGG‑A‑GGG‑GGGGTatatat                                                                                                                  <  1:158445/141‑1 (MQ=255)

               tAAAATTCCTCCAATAATTTTTAAGGAGTCAATCAATATCATATAGGTTAAACTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAGAATGGGG‑AGGGG‑GGGGTATATATTGa                                                                                                               <  2:241672/141‑1 (MQ=255)

                aaaaTTCCTCCAATAATTTTTAAGGAGTCAATCAATATCATATAGGTTAAACTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGG‑AGGGG‑GGGGTATATATTGAt                                                                                                              >  1:338317/1‑141 (MQ=255)

                    ttCCTCCAATAATTTTTAAGGAGTCAATCAATATCATATAGGTTAAACTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGG‑A‑GGG‑GGGGTATATATTGATACCTa                                                                                                         <  1:56905/141‑1 (MQ=255)

                     tcctccAATAATTTTTAAGGAGTCAATCAATATCATATAGGTTAAACTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAACATGGGG‑A‑GCG‑GGGGCATAGACTGATACCTAc                                                                                                        >  2:243727/1‑141 (MQ=255)

                        tccAATAATTTTTAAGGAGTCAATCAATATCATATAGGTTAAACTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGG‑A‑GGG‑GGGGTATATATTGATACCTACGCt                                                                                                     >  1:86875/1‑141 (MQ=255)

                             taatTTTTAAGGAGTCAATCAATATCATATAGGTTAAACTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGG‑AGGGG‑GGGGTATATATTGATACCTACGCTagaa                                                                                                 <  2:283703/141‑1 (MQ=255)

                             aaatTTTTAAGGAGTCAATCAATATCATATAGGTTAAACTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAAAAAAAAATGGGG‑AGGGG‑GGGGTATATATTGATACCTACGCTagaa                                                                                                 <  2:9509/140‑1 (MQ=255)

                              aatTTTTAAGGAGTCAATCAATATCATATAGGGTAAACTAACTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGG‑AGGGG‑GGGGTATATATTGATACCTACGCTagaag                                                                                                <  1:40705/141‑1 (MQ=255)

                                                       atatAGGTTAAACTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGG‑AGGGG‑GGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACtt                                                                       >  1:363305/1‑141 (MQ=255)

                                                        tataGGTTAACCTATCTTCAATTGATTGCTAGAATAAGTATAAGAAACACTTTATGCATAAATATACAACAATAAATGCGG‑A‑GGG‑GGGGTATATATTGATACCTACGCTATAAGAAATTATTGTTAAGTATGGAAACTTAg                                                                     <  2:22352/141‑1 (MQ=255)

                                                            ggTTAAACTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGG‑AGGGG‑GGGGTCTATATGGATACCTAAGCTAGAAGAAAGTATTGAAAAGAATGGAAACATAGTTg                                                                  >  2:353979/1‑141 (MQ=255)

                                                             gTTAAACTATCTTCACTTGGTTGAAATAATAAGCATAAATGAAGCATGATGATTAGACGCGGAACAAAAAATGGGGCG‑GGG‑GGGGTATATATTGATCCCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGa                                                                 <  1:8567/141‑1 (MQ=255)

                                                                     atcccaagttgtgtgCTATAATAAGCATAAGTGAAGCAGTATGTTTATACGCGGAACAAAAAATGGGG‑AGGGG‑GGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGa                                                         <  2:355677/128‑1 (MQ=255)

                                                                     aTCTTCAATTGATTGCTATAGTAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGG‑A‑GGG‑GGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTCAGTTGATTATTTGaa                                                        >  1:247245/1‑141 (MQ=255)

                                                                          cAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGG‑A‑GGG‑GGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTg                                                   <  1:80212/141‑1 (MQ=255)

                                                                          cAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGG‑A‑GGG‑GGGGTATATATTGATACCGACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTg                                                   <  1:54290/141‑1 (MQ=255)

                                                                           aaTTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGG‑AGGGG‑GGGGTATATATTGATACCTACGCTAGAAGAGATTATTGATAAGTATGGAAACTTGGTTGATTATTTGAAATTTg                                                   >  2:114585/1‑141 (MQ=255)

                                                                           aaTTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGG‑AGGGG‑GGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTg                                                   >  2:253406/1‑141 (MQ=255)

                                                                             ttgattgCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGG‑A‑GGG‑GGGGTATATATTGATACCTACGCTAGAAGAAATTATTGGTAAGTTTGGAAACTTAGTTGGATATTTGAAAtttattt                                                >  2:23495/1‑137 (MQ=255)

                                                                                attgCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGG‑AGGGG‑GGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGTa                                              >  1:270982/1‑141 (MQ=255)

                                                                                                       aGCATTATGATTAGACGCGGAACAAAAAATGGGG‑AGGGG‑GGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGTAACAGTTGAGGTTTATGAAGAttt                       >  1:383707/1‑141 (MQ=255)

                                                                                                          aTTATGACTAGAAGAAGAAAGAAAAATGGGG‑A‑GGGTGGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGTAACAGTTGAGGTTTATGAAGATttgtt                    <  2:212090/141‑1 (MQ=255)

                                                                                                              tGATTAGACGCGGAACAAAAAATGGGG‑AGGGG‑GGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGTAACAGTTGAGGTTTATGAAGATTTGTTGtta                <  1:355663/141‑1 (MQ=255)

                                                                                                                 ttAGACGCGGAACAAAAAATGGGG‑A‑GGG‑GGGGTATATATTGATACCTACGATAGAAGAAATTAGTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGTAACAGTTGAGGTTTATGAAGATTTGTTGTTATTaa            >  2:290586/1‑141 (MQ=255)

                                                                                                                            aCAAAAAATGGGG‑AGGGG‑GGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAACTTTGATGTAACAGTTGAGGTTTATGAAGATTTGTTGTTATTAAGAAGTTTAAg  <  1:264973/141‑1 (MQ=255)

ATTTCTTATTCATTTTAAAATTCCTCCAATAATTTTTAAGGAGTCAATCAATATCATATAGGTTAAACTATCTTCAATTGATTGCTATAATAAGCATAAATGAAGCATTATGATTAGACGCGGAACAAAAAATGGGG‑A‑GGG‑GGGGTATATATTGATACCTACGCTAGAAGAAATTATTGATAAGTATGGAAACTTAGTTGATTATTTGAAATTTGATGTAACAGTTGAGGTTTATGAAGATTTGTTGTTATTAAGAAGTTTAAG  >  CP000730/51190‑51453

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