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 F18 I0 R2	18	11.5	256338	98.4%	252236	141.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,010,695	T→A	33.5%	L35L (CTA→CTT)	USA300HOU_RS10125 ←	Putative multidrug export ATP‑binding/permease protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,010,695	0	T	A	33.5%	7.1 / 10.0	12	L35L (CTA→CTT)	USA300HOU_RS10125	Putative multidrug export ATP‑binding/permease protein
Reads supporting (aligned to +/- strand): ref base T (5/3); new base A (2/2); total (7/5)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.20e-01

TTCAATTGGTGGTCTCACTATTACAAAAATAAATAATGCGATACCAATGGCAATAGTTAAATGATGAACTTTTTCATCAGTCGTTAGTGCGTGGTTATTAATCACGCCATCTATTGCATATTTAATTAATAGTGGTATAAGCATTGGTATACCAAACTTAATTATCCCAACAATAATCGTTGCAAAAATACGATATTTGTATGGCTTAACAAATTGCAAATATCGTTTAATCATACAATCCCCCCTAATCTATTGCCCTATCCTATTC  >  USA300TCH1516_ALE/2010566‑2010833

ttCAATTGGTGGTCTCACTATTACAAAAATAAATAATGCGATACCAATGGCAATAGTTAAATGATGAACTTTTTCATCAGTCGTTAGTGCGTGGTTATTAATCACGCCATCTATTGCATATTTAATTAATAGTGGTATAAg                                                                                                                                 >  2:89149/1‑141 (MQ=255)

        gtggtCTCACTATTACAAAAATAAATAATGCGATACCAATGGCAATAGTTAAATGATGAACTTTTTCATCAGTCGTTAGTGCGTGGTTATTAATCACGCCATCTATTGCATATTTAATTAATAGTGGTATAAGCATTGGta                                                                                                                         >  1:115996/1‑141 (MQ=255)

          ggtCTCACTATTACAAAAATAAATAATGCGATACCAATGGCAATAGTTAAATGATGAACTTTTTCATCAGTCGTTAGTGCGTGGTTATTAATCACGCCATCTATTGCATATTTAATTAAAAGTGGTATAAGCATTGGtata                                                                                                                       >  2:102954/1‑141 (MQ=255)

          ggtCTCACTATTACAAAAATAAATAATGCGATACCAATGGCAATAGTTAAATGATGAACTTTTTCATCAGTCGTTAGTGCGTGGTTATTAATCACGCCATCTATTGCATATTTAATTAAAAGTGGTATAAGCATTGGtata                                                                                                                       >  2:65440/1‑141 (MQ=255)

              tcACTATTACAAAAATAAATAATGCGATACCAATGGCAATAGTTAAATGATGAACTTTTTCATCAGTCGTTAGTGCGTGGTTATTAATCACGCCATCTATTGCATATTTAATTAATAGTGGTATAAGCATTGGTATACCaa                                                                                                                   >  2:77727/1‑141 (MQ=255)

                                           ccAATGGCAATAGTTAAATGATGAACTTTTTCATCAGTCGTTAGTGCGTGGTTATTAATCACGCCATCTATTGCATATTTAATTAATAGTGGTATAAGCATTGGTATACCAAACTTAATTATCCCAACAATAATCGTTGCa                                                                                      <  2:100791/141‑1 (MQ=255)

                                                                            tcaGTCGTTAGTGCGTGGTTATTAATCACGCCATCTATTGCATATTTAATTAATAGTGGTATAAGCATTGGTATACCAAACTTAATTATCCCAACAATAATCGTTGCAAAAATACGATATTTGTATGGCTTAACAAATTGc                                                     >  1:81200/1‑141 (MQ=255)

                                                                                      gTGCGTGGTTATTAATCACGCCATCTATTGCATATTTAATTAAAAGTGGTATAAGCATTGGTATACCAAACTTAATTATCCCAACAATAATCGTTGCAAAAATACGATATTTATATGGCTTAACAAATTGCAAATATCGtt                                           <  1:102954/141‑1 (MQ=255)

                                                                                      gTGCGTGGTTATTAATCACGCCATCTATTGCATATTTAATTAAAAGTGGTATAAGCATTGGTATACCAAACTTAATTATCCCAACAATAATCGTTGCAAAAATACGATATTTATATGGCTTAACAAATTGCAAATATCGtt                                           <  1:65440/141‑1 (MQ=255)

                                                                                                          ccATCTATTGCATATTTAATTAATAGTGGTATAAGCATTGGTATACCAAACTTAATTATCCCAACAATAATCGTTGCAAAAATACGATATTTGTATGGCTTAACAAATTGCAAATATCGTTTAATCATACAATCCCCCCTa                       >  2:16098/1‑141 (MQ=255)

                                                                                                           cATCTATTGCATATTTAATTAATAGTGGTATAAGCATTGGTATACCAAACTTATTTATCCCAACAATAATCGTTGCAAATATACGATATTTGTATGGCTTAACAAATTGCAAATATCGTTTAATCATACAATCCCCCCTaa                      <  2:115996/141‑1 (MQ=255)

                                                                                                                aTTGCATATTTAATTAATAGTGGTATAAGCATTGGTATACCAAACTTAATTATCCCAACAATAATCGTTGCAAAAATACGATATTTGTATGGCTTAACAAATTGCAAATATCGTTTAATCATACAATCCCCCCTAATCTAt                 <  1:77727/141‑1 (MQ=255)

                                                                                                                               aatAGTGGTATAAGCATTGGTATACCAAACTTAATTATCCCAACAATAATCGTTGCAAAAATACGATATTTGTATGGCTTAACAAATTGCAAATATCGTTTAATCATACAATCCCCCCTAATCTATTGCCCTATCCTATTc  >  1:40167/1‑141 (MQ=255)

TTCAATTGGTGGTCTCACTATTACAAAAATAAATAATGCGATACCAATGGCAATAGTTAAATGATGAACTTTTTCATCAGTCGTTAGTGCGTGGTTATTAATCACGCCATCTATTGCATATTTAATTAATAGTGGTATAAGCATTGGTATACCAAACTTAATTATCCCAACAATAATCGTTGCAAAAATACGATATTTGTATGGCTTAACAAATTGCAAATATCGTTTAATCATACAATCCCCCCTAATCTATTGCCCTATCCTATTC  >  USA300TCH1516_ALE/2010566‑2010833

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A