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	39,195	T→C	62.2%	K647E (AAA→GAA)	mecA ←	penicillin binding protein 2 prime

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	39,195	0	T	C	62.2%	19.3 / 28.0	32	K647E (AAA→GAA)	mecA	penicillin binding protein 2 prime
Reads supporting (aligned to +/- strand): ref base T (9/3); new base C (8/12); total (17/15)
Fisher's exact test for biased strand distribution p-value = 7.59e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.89e-01

AGCACTTATTAATAATTCATAATAAAACAGTGAAGCAACCATCGTTACGGATTGCTTCACTGTTTTGTTATTCATCTATATCGTATTTTTTATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTTGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTG  >  CP000730/39060‑39332

aGCAATTATTAATTATTCATAATAAAACAGTGAAGCAACCATCGTTACGGATTGCTTCACTGTTTTGTTATTCATCTATATCGTATTTTTTATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTTGGCAt                                                                                                                                      <  2:284965/141‑1 (MQ=255)

     aaaataagaaTTCATAATAAATCAGTGAAGAAACCATCGTTACGGATTGATTCACTGTTTTGTTATTCATCTATATCGTATTTTTTATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTTGGCATTGtag                                                                                                                                 <  1:93683/137‑1 (MQ=255)

                  aaaataaAACAGTGAAGCATCCATCGTTACGGATTACATCAATGTTTTGTTATTCATCTATATCGTATTTTTTATTACCGTTCTCATATAGCTCATCATACACTTTACCTGATTTGTCTTCATTGTAGCTAGCCATTCCtt                                                                                                                    <  1:94399/139‑1 (MQ=255)

                       aaaaCAGGGAAGCAACCATCGTTACGGATTACTTCACTGTTTTGTTATTCATCTATATCGTATTTTTTATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTCGGCATTGTAGCTAGCCATTCCTTTATCt                                                                                                               <  1:155145/141‑1 (MQ=255)

                            aGTGAAGCAACCATCGTTACGGATTGCTTCACTGTTTTGTTATTCATCTATATCGTATTTTTTATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTCGGCATTGTAGCTAGCCATTCCTTTATCTTGTAc                                                                                                          >  1:8388/1‑141 (MQ=255)

                                   cAACCATCGTTACGGATTGCTTCACTGTTTTGTTATTCATCTATATCGTATTTTTTATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTTGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTa                                                                                                   <  2:74352/141‑1 (MQ=255)

                                           gtaaCGGATTGCTTCACTGTTTTGTTATTCACCTATATCGTATTTTTTATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTCGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAAt                                                                                           <  1:133355/138‑1 (MQ=255)

                                           gTTACGGATTGCTTCACTGTTTTGTTATTCATCTATATCGTATTTTTTATTACCGTTCTCATATAGCTCATCATACACTTTACCTGCGATTTCGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAAt                                                                                           >  1:275704/1‑141 (MQ=255)

                                           gTTACGGATTGCTTCACTGTTTTGCTATTCATCTATATCGTATTTTTTATTACCGTTCTCATATAGCTCATCATACACTGTACCTGAGATTTCGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAAt                                                                                           >  1:288265/1‑141 (MQ=255)

                                                    tGCTCCACTTTTTTGTTATTTATCTAAATCGTATTTTTTATTACCCTGCTCATATAGCTCATCATACACTTTACCTGAGATTTCGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCcatcat                                                                                  <  2:95746/141‑1 (MQ=255)

                                                           ctattttGTTATTCATCTATATCGTATTTTTTATTACCGTTCTAATATAGCTCATCATACACTTTACCTGAGATTTCGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCCATCATCATGttt                                                                           <  1:84529/138‑1 (MQ=255)

                                                               tttGTTATTCATCTATATCGTATTTTTTATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTCGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATATTTAACATTAATAGCCATCATCATGTTTGGAt                                                                       >  1:51890/1‑141 (MQ=255)

                                                                ttGTTATTCATCTATATCGTATTTTTTATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTTGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGAtt                                                                      >  1:142979/1‑141 (MQ=255)

                                                                       tCATCTATATCGTATTTTTTATTACGGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTCGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCCTTTATCTTGTTTCGATTATCtttt                                                               >  1:371477/1‑140 (MQ=255)

                                                                                  ggaTTTTTTAGTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTCGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGAATTATCTTTATCATATGatat                                                    <  2:143104/139‑1 (MQ=255)

                                                                                     ttttttATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTTGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATaaa                                                 >  1:142139/1‑141 (MQ=255)

                                                                                         ttattaCCGTTCTCATATACCGCATCATACACTTTACCTGAGATTTCGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAaccac                                             <  2:13775/141‑1 (MQ=255)

                                                                                                       atatAGCTCATCATACACTTTACCTGAGATTTTGGCATTGTAGCTAGACATTCCTTTATCTTGTACATCTTTAACATTAATAGCCGTCATCATGTTTGGATTATCTTTATCGTATCATATAAACCACCCACTTTGTCTGcc                               >  2:386876/1‑141 (MQ=255)

                                                                                                         ataGCTCATGCTACACTTTACCTGAGATTTTGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAg                             >  1:290070/1‑141 (MQ=255)

                                                                                                           aGCTCATCATACACTTTACCTGAGATTTCGGCATTGTAGCTAGCCATTCCTTCATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTACCAGtt                           <  2:248697/141‑1 (MQ=255)

                                                                                                                atcatACACTTTACCTGAGATTTCGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTcc                      >  1:204308/1‑141 (MQ=255)

                                                                                                                   ttACACTTTACCTGGGATTTCGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTg                   <  2:1055/140‑1 (MQ=255)

                                                                                                                    tgcacTTTACCTGAGGTTTTGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAGCATTAATAGCCATCATCATGTTTGGCTTATCATTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGt                  >  1:186975/3‑141 (MQ=255)

                                                                                                                     acacTTTACCTGAGATTTTGGCCTTGTAACTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTGGGATTATCTTTATCATATGATATAAACCACGCAATTTGTCTGCCAGTTTCTGCTTGtt                 >  1:29482/1‑141 (MQ=255)

                                                                                                                     acacTTTACCTGAGATTTTGGCATTGTAGCTAGCCATTGCTTTATCTTGTATATATTTCCAATTCATAGCCCTCGTCATGTTTGGATTATCTTTAGCATATTATATAAACCACCCAATTTGTTCGCCAGTTTCTACTTGtt                 >  2:229832/1‑141 (MQ=255)

                                                                                                                     acacTTTACCTGAGATTTCGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATGGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTTTCTGCCAGTTTCTCCTTGtt                 >  1:170886/1‑141 (MQ=255)

                                                                                                                      accgtcgccTGAGATTTCGGCATTGTAGCTAGCCATTCCTTTATTATGTACATCTTTAACATTAATAGCCATCATCATGTTTGGGTTATCTTTATCATATGATAGAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGgtt                <  2:4330/134‑1 (MQ=255)

                                                                                                                       acTTTACCTGAGATTTTGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTTTCATATGATATAAACCACCCAATTTGTCTGCCGGTTTCTCCTTGtttt               >  2:270932/1‑140 (MQ=255)

                                                                                                                       acTTTACCTGAGATTTTGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTCCCACCTTCTCCTTCTTTc               >  2:333878/1‑141 (MQ=255)

                                                                                                                           tACCGGCGATTTCGGCCTTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTACCATTAATAGCCATCATCATGTTTGGATTAACTCTATAATACGATCTCAACCACCCAATTAGTCTACCATTTTCTCCTTGTTTCtttt           <  2:331242/141‑1 (MQ=255)

                                                                                                                                gagaTTTCGGCATTGTAGCTAGCCTTTCCTTTATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCTTTTTgtgt      >  1:192116/1‑141 (MQ=255)

                                                                                                                                  gaTTTCGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTc    <  1:29841/141‑1 (MQ=255)

                                                                                                                                    tttcGGTATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTTTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTg  <  2:345967/141‑1 (MQ=255)

AGCACTTATTAATAATTCATAATAAAACAGTGAAGCAACCATCGTTACGGATTGCTTCACTGTTTTGTTATTCATCTATATCGTATTTTTTATTACCGTTCTCATATAGCTCATCATACACTTTACCTGAGATTTTGGCATTGTAGCTAGCCATTCCTTTATCTTGTACATCTTTAACATTAATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTG  >  CP000730/39060‑39332

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