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	26	27.1	575272	96.9%	557438	141.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP000730	39,378	C→A	D586Y (GAT→TAT)	mecA ←	penicillin binding protein 2 prime

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	39,378	0	C	A	100.0%	52.6 / NA	16	D586Y (GAT→TAT)	mecA	penicillin binding protein 2 prime
Reads supporting (aligned to +/- strand): ref base C (0/0); new base A (9/7); total (9/7)

TAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATCTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTGTCTTTTAATAAGTGAGGTGCGTTAATATTGCCATT  >  CP000730/39243‑39513

tAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATattctt                                                                                                                                    >  1:138275/1‑141 (MQ=255)

                    ttATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGAATAAGATCTGTAAATAGATACTTTATGTGTTTTATTTACGACt                                                                                                                >  1:226570/1‑141 (MQ=255)

                                tatGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCa                                                                                                    >  2:19521/1‑141 (MQ=255)

                                     tataAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTTCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGt                                                                                               >  1:76681/1‑141 (MQ=255)

                                     tataAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGt                                                                                               <  2:22380/141‑1 (MQ=255)

                                                   tttGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGatat                                                                                 <  2:286864/141‑1 (MQ=255)

                                                     tGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATAttt                                                                               >  2:65446/1‑141 (MQ=255)

                                                      gTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATAtttt                                                                              >  1:196594/1‑141 (MQ=255)

                                                                             aTTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTttcttc                                                       >  2:23756/1‑141 (MQ=255)

                                                                             aTTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTttcttc                                                       >  1:139671/1‑141 (MQ=255)

                                                                                ttGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCaa                                                    <  1:74063/141‑1 (MQ=255)

                                                                                   aGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACt                                                 <  2:186013/141‑1 (MQ=255)

                                                                                       tttctgaaCCTGACTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGt                                             <  2:226570/134‑1 (MQ=255)

                                                                                           aGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGttttt                                         <  2:16416/141‑1 (MQ=255)

                                                                                               ccGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCgtg                                     >  2:1010/1‑141 (MQ=255)

                                                                                                            ttAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTGTCTTTTAATAAGt                        <  1:52364/141‑1 (MQ=255)

                                                                                                                                  aaTATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTGTCTTTTAATAAGTGAGGTGCGTTAATATTGCCatt  >  1:82734/1‑141 (MQ=255)

TAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATCTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTGTCTTTTAATAAGTGAGGTGCGTTAATATTGCCATT  >  CP000730/39243‑39513

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `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