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
A23 F110 I1 R1	27	27.0	575272	98.6%	567218	141.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	2,483,375	G→T	V45F (GTC→TTC)	USA300HOU_RS12790 →	putative HTH‑type transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,483,375	0	G	T	100.0%	55.8 / NA	16	V45F (GTC→TTC)	USA300HOU_RS12790	putative HTH‑type transcriptional regulator
Reads supporting (aligned to +/- strand): ref base G (0/0); new base T (12/4); total (12/4)

TTTATTTATCAATGCAAATGAGACGGAATCTTATATTGATATACATGCACCTAAAATGAATGATAACGTTCAAAGTATTATTAATGCAGTCAATGATTTAGACAAATCACATACATTAGTCGGATACATAGACAAAGAAATCCATATCATTAATGTATCAGATGTTATAACATTCCAAGTTATTAATAAAAATGTAACAGCCATTACAAGCAATCAAAAATTCAAACTAAAATTACGACTTTAT  >  USA300TCH1516_ALE/2483257‑2483500

tttatttaTCAATGCAAATGAGACGGAATCTTATATTGATATACATGCACCTAAAATGAATGATAACGTTCAAAGTATTATTAATGCAGTCAATGATTTAGACAAATCACATACATTATTCGGATACATAGACAAAGAAAt                                                                                                         <  1:219177/141‑1 (MQ=255)

      tatCAATGCAAATGAGACGGAATCTTATATTGATATACATGCACCTAAAATGAATGATAACGTTCAAAGTATTATTAATGCAGTCAATGATTTAGACAAATCACATACATTATTCGGATACATAGACAAAGAAATCCatat                                                                                                   >  1:115542/1‑141 (MQ=255)

                 aTGAGACGGAATCTTATATTGATATACATGCACCTAAAATGAATGATAACGTTCAAAGTATTATTAATGCAGTCAATGATTTAGACAAATCACATACATTATTCGGATACATAGACACAGAAATCCATATCATTAATGTAt                                                                                        >  2:92706/1‑141 (MQ=255)

                   gagaCGGAATCTTATATTGATATACATGCACCTAAAATGAATGATAACGTTCAAAGTATTATTAATGCAGTCAATGATTTAGACAAATCACATACATTATTCGGATACATAGACAAAGAAATCCATATCATTAATGTATCa                                                                                      >  1:86250/1‑141 (MQ=255)

                        ggAATCTTATATTGATATACATGCACCTAAAATGAATGATAACGTTCAAAGTATTATTAATGCAGTCAATGATTTAGACAAATCACATACATTATTCGGATACATAGACAAAGAAATCCATATCATTAATGTATCAGATGt                                                                                 <  1:41584/141‑1 (MQ=255)

                        ggAATCTTATATTGATATACATGCACCTAAAATGAATGATAACGTTCAAAGTATTATTAATGCAGTCAATGATTTAGACAAATCACATACATTATTCGGATACATAGACAAAGAAATCCATATCATTAATGTATCAGATGt                                                                                 >  2:210179/1‑141 (MQ=255)

                                atatTGATATACATGCACCTAAAATGAATGATAATGTTCAAAGTATTATTAATGCAGTCAATGATTTAGACAAATCACATACATTATTCGGATACATAGACAAAGAAATCCATATCATTAATGTATCAGATGTTATAACAt                                                                         <  1:147699/141‑1 (MQ=255)

                                 tatTGATATACATGCACCTAAAATGAATGATAACGTTCAAAGTATTATTAATGCAGTCAATGATTTAGACAAATCACATACATTATTCGGATACATAGTCAAAGAAATCCATATCATTAATGTATCAGATGTTATAACAtt                                                                        >  2:239280/1‑141 (MQ=255)

                                       tataCATGCACCTAAAATGAATGATAACGTTCAAAGTATTATTAATGCAGTCAATGATTTAGACAAATCACATACATTATTCGGATACATAGACAAAGAAATCCATATCATTAATGTATCAGATGTTATAACATTCCAAGt                                                                  >  1:228355/1‑141 (MQ=255)

                                                           atgaTAACGTTCAAAGTATTATTAATGCAGTCAATGATTTAGACAAATCACATACATTATTCGGATACATAGACAAAGAAATCCATATCATTAATGTATCAGATGTTATAACATTCCAAGTTATTAATAAAAATGTAACAg                                              >  1:115743/1‑141 (MQ=255)

                                                           atgaTAACGTTCAAAGTATTATTAATGCAGTCAATGATTTAGACAAATCACATACATTATTCGGATACATAGACAAAGAAATCCATATCATTAATGTATCAGATGTTATAACATTCCAAGTTATTAATAAAAATGTAACAg                                              >  1:170758/1‑141 (MQ=255)

                                                              aTAACGTTCAAAGTATTATTAATGCAGTCAATGATTTAGACAAATCACATACATTATTCGGATACATAGACAAAGAAATCCATATCATTAATGTATCAGATGTTATAACATTCCAAGTTATTAATAAAAATGTAACAGCCa                                           >  2:62368/1‑141 (MQ=255)

                                                                                ttaATGCAGTCAATGATTTAGACAAATCACATACATTATTCGGATACATAGACAAAGAAATCCATATCATTAATGTATCAGATGTTATAACATTCCAAGTTATTAATAAAAATGTAACAGCCATTACAAGCAATCAAAAAt                         >  1:28392/1‑141 (MQ=255)

                                                                                                  tAGACAAATCACATACATTATTCGGATACATAGACAAAGAAATCCATATCATTAATGTATCAGATGTTATAACATTCCAAGTTATTAATAAAAATGTAACAGCCATTACAAGCAATCAAAAATTCAAACTAAAATTACGAc       >  1:232725/1‑141 (MQ=255)

                                                                                                     aCAAATCACATACATTATTCGGATACATAGACAAAGAAATCCATATCATTAATGTATCAGATGTTATAACATTCCAAGTTATTAATAAAAATGTAACAGCCATTACAAGCAATCAAAAATTCAAACTAAAATTACGACttt    <  1:130531/141‑1 (MQ=255)

                                                                                                       aaaTCACATACATTATTCGGATACATAGACAAAGAAATCTATATCATTAATGTATCAGATGTTATAACATTCCAAGTTATTAATAAAAATGTAACAGCCATTACAAGCAATCAAAAATTCAAACTAAAATTACGACTTTAt  >  1:898/1‑141 (MQ=255)

TTTATTTATCAATGCAAATGAGACGGAATCTTATATTGATATACATGCACCTAAAATGAATGATAACGTTCAAAGTATTATTAATGCAGTCAATGATTTAGACAAATCACATACATTAGTCGGATACATAGACAAAGAAATCCATATCATTAATGTATCAGATGTTATAACATTCCAAGTTATTAATAAAAATGTAACAGCCATTACAAGCAATCAAAAATTCAAACTAAAATTACGACTTTAT  >  USA300TCH1516_ALE/2483257‑2483500

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A