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
A15 F177 I0 R1	51	26.9	575130	96.6%	555575	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	2,018,733:1	(A)_6→7	100%	coding (186/810 nt)	USA300HOU_1869 ←	transglycosylase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,018,727	1	.	A	91.7%	28.2 / ‑2.5	12	coding (192/810 nt)	USA300HOU_1869	transglycosylase
Reads supporting (aligned to +/- strand): ref base . (1/0); new base A (4/7); total (5/7)
Fisher's exact test for biased strand distribution p-value = 4.17e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.41e-01
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.
Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch.

TGATGATTGTAGAATCGTTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGTTATCAGCTGACACAAAACTACTTTTATTTTCAATTTTTCTTAGTTCATCCACATTATCGCGTGTAGAT‑AAAAA‑ATACATGATACCAATAAACAATGCGATAATGATTAGAATGGTTAATAATATTTTTAATAGTATTCGTTTACTTTTTTTCTTTTTCGGCGGTTTGCCAACTGGTTGATAATACGTATTATAGTGAGG  >  CP000730/2018596‑2018858

tgatgaTTGTAGAATCGTTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGTTATCAGCTGACACAAAACTACTTTTATTTTCAATTTTTCTTAGTTCATCCACATTATCGCGTGTAGAT‑aaaaa‑aata                                                                                                                            <  2:155088/141‑4 (MQ=255)

    gatTGTAGAATCGTTCATCTTCCATTGAAATAGAGGCACCTTTAATATACTCTGGCATGTTATCAGCTGACACAAAACTACTTTTATTTACAATTTTTCTTAGTTCATCCACATTATCGCGTGTAGATAAAAAA‑ATACATg                                                                                                                         >  1:205625/1‑141 (MQ=255)

       tGTAGAATCGTTCATCTTCCATTGAAATAAAGGCACCTTTACCATACTCTGGCATGTTATCAGCTGACACAAAACTACTTTTATTTTCAATTTTTCTTAGTTCATCCTCATTATCGCGTGTAGATAAAAAA‑ATACATGATa                                                                                                                      >  1:282214/1‑141 (MQ=255)

                               aaaTAAAGGCACCTTTAACATCCTCTGGCATGTTATCAGATGACACAACACTACTTTTATTTTCAATTTTTCTTAGTTCACCCACATTATCGCGTGTAAATAAAAAA‑ATACATGATACCAATAAACAATGCGATAATGAtt                                                                                              <  2:225436/141‑1 (MQ=255)

                                  tAAAGGCACCTTTAACATACTCTGGCATGTTATCAGCTGACACAAAACTACTTTTATTTTCAATTTTTCTTAGTTCATCCACATTATCGCGTGTAGATAAAAAA‑ATACATGATACCGATAAACAATGCGATAATGGTTAGa                                                                                           >  1:59690/1‑141 (MQ=255)

                                      ggCACCTTTAACATACTCTGGCATGTTATCAGCTGACACAAAACTACTTTTATTTTCAATTTTTCTTAGTTCATCCACATTATCGCGTGTCGAT‑AAAAACATACCTGATACCAATAAACAATGCGATAATgctgaacagga                                                                                       >  1:141580/1‑131 (MQ=255)

                                                      tctGGCATGTTAGCAGCTGACACAAAACTACTTTTATTTTCAATTTTTCTTAGTTCATCCACATTATCGCGTGTAGATAAAAAA‑ATACATGATTCCAATACACAATGCGATAATGATTAGAATGGTTAATAATATTTTTaa                                                                       <  2:233934/141‑1 (MQ=255)

                                                                 aTCAGCTGACACAAAACTACTTTTATTTTCAATTTTTCTTAGTTCATCCACATTATCGCGTGTAGATAAAAAA‑ATACATGATACCAATAAACAATGAGATAATGACTAGAATAGTAAATAATATGCATAATAGTATTCGtt                                                            >  2:260924/1‑141 (MQ=255)

                                                                                          ttttCAATTTTTCTTAGTTCATCCACATTATCGCGTGTAGATAAAAAA‑ATACATGATACCAATAAACAATGCGATAATGATTAGAATGGTTAATAATATTTTTAATAGTATTCGTTTACTTTTTTTCTTTTTCGGCGGttt                                   <  1:10804/141‑1 (MQ=255)

                                                                                                  ttttCTTAGTTCATCCACATTATCGCGTGTAGATAAAAAA‑ATACATGATACCAATAAACAGTGCGATAATGATTAGAATGGTTAATAATATTTTTAATAGTATTCGTTTACTTTTTTTCTTTTTCGGCGGTTTGCCAACTg                           <  2:205625/141‑1 (MQ=255)

                                                                                                        tAGTTCATCCACATTATCGAGTGTATATAAAAAA‑ATACATGATACCAATAAACAATGCGATAATGATTAGAATGGTTAATAATATTTTTAATAGTATTCGTTTACTTTTTTTCTTTTTCGGCGGTTTGCCAACTGGTTGat                     <  1:836/141‑1 (MQ=255)

                                                                                                                 cacaTTATTGCGTGTAGTTAAAAAA‑ATACATGATACCAATAAACAATGCGATAATGATTAGAATGGTTAATAATATTTTTAATAGTATTCGTTTACTTTTTTTCTTTTTCGGCGGTTTGCCAACTGGTTGATAATACGtat            <  1:76606/141‑1 (MQ=255)

                                                                                                                           cgTTTAGATAAAAAA‑ATACATGATACCAATAAACAATGCGATAATGATTAGAATGGTTAATAATATTTTTAATAGTATTCGTTTACTTTTTTTCTTTTTCGGCGGTTTGCCAACTGGTTGATAATACGTATTATAGTGAgg  <  1:113506/141‑1 (MQ=255)

TGATGATTGTAGAATCGTTCATCTTCCATTGAAATAAAGGCACCTTTAACATACTCTGGCATGTTATCAGCTGACACAAAACTACTTTTATTTTCAATTTTTCTTAGTTCATCCACATTATCGCGTGTAGAT‑AAAAA‑ATACATGATACCAATAAACAATGCGATAATGATTAGAATGGTTAATAATATTTTTAATAGTATTCGTTTACTTTTTTTCTTTTTCGGCGGTTTGCCAACTGGTTGATAATACGTATTATAGTGAGG  >  CP000730/2018596‑2018858

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