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
A17 F172 I1 R2	29	34.5	745914	96.0%	716077	139.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP000730	463,014	C→A	E47* (GAA→TAA)	USA300HOU_0437 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	463,014	0	C	A	100.0%	97.6 / NA	30	E47* (GAA→TAA)	USA300HOU_0437	hypothetical protein
Reads supporting (aligned to +/- strand): ref base C (0/0); new base A (21/9); total (21/9)

GTCTTGTTTAGCTTTGTTGATAATGTCTTTGATTGAATGTAGTCCTTTATCGGCGAAGTATGATCTTAAGTTGTCTTTTGTAGCTTGGTCAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTCTAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCATATCCAACAACGCCAGTTGCTAAAACACCTACCATTGCCGTAGCTACTAAAACCTTTTTAAATTTC  >  CP000730/462880‑463150

gTCTTGTTTAGCTTTGTTGATAATGTCTTTGATTGAATGTAGTCCTTTATCGGCGAAGTATGATCTTAAGTTGTCTTTTGTAGCTTGGTCAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTATaagaa                                                                                                                                    >  1:15267/1‑141 (MQ=255)

       ttAGCTTTGTTGATAATGTCATTGATTGAATGTAGTCCTTTATCGGCGAAGTATGATCTTAAGTTGTCTTTTGTAGCTTGGTCAGCATTCTTATCTAATAAAACATCAATATAACTTAATTCATGTTATAAGAAGTTTGca                                                                                                                             >  2:131616/1‑141 (MQ=255)

                         tCTTTGATTGAATGTAGTCCTTTATCGGCGAAGTATGATCTTAAGTTGTCTTTTGTAGCTTGGTCAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGt                                                                                                           <  2:67673/141‑1 (MQ=255)

                              gattgaATGTCGTCCTTTATCGGCGAAGTATGATCTTAAGTTGTCTTTTGTAGCTTGGTCAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCAtt                                                                                                      <  1:74577/141‑1 (MQ=255)

                              gattgaATGTAGTCCTTTATCGGCGAAGTATGATCTTAAGTTGTCTTTTGTAGCTTGGTCAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCAtt                                                                                                      >  1:26976/1‑141 (MQ=255)

                                    aTGTAGTCCTTTATCGGCGAAGTATGATCTTAAGTTGTCTTTTGTAGCTTGGTCAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTgaga                                                                                                >  2:245414/1‑141 (MQ=255)

                                         gTCCTTTATCGGCGAAGTATGATCTTAAGTTGTCTTTTGTAGCTTGGTCAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTATAAGACGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATaaa                                                                                           >  2:60015/1‑141 (MQ=255)

                                         gTCCTTTATCGGCGAAGTATGATCTTAAGTTGTCTTTTGTAGCTTGGTCAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATaaa                                                                                           >  1:19298/1‑141 (MQ=255)

                                             tttATCGGCGAAGTATGATCTTAAGTTGTCTTTTGTAGCTTGGTCAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACttt                                                                                       <  1:316737/141‑1 (MQ=255)

                                                  cGGCGAAGTATGATCTTAAGTTGTCTTTTGTAGCTTGGTCAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTATAAGAAGTTTGCATAATCATATAGTACGAGTCCATTTTGAGAATAAACTTTCGCAt                                                                                  <  2:16628/141‑1 (MQ=255)

                                                          tATGATCTTAAGTTGTCTTTTGTAGCTTGGTCAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGa                                                                          >  1:296063/1‑141 (MQ=255)

                                                                 ttAAGTTGTCTTTTGTAGCTTGGTCAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCat                                                                   >  1:10453/1‑141 (MQ=255)

                                                                    aGTTGTCTTTTGTAGCTTGGTCAGCATTCTTATCTAATAACACATCAATATAACTTAATTTATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCATATc                                                                >  1:276403/1‑141 (MQ=255)

                                                                       tGTCTTTTGTAGCTTGGTCAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCATATCcaa                                                             >  1:78409/1‑141 (MQ=255)

                                                                       tGTCTTTTGTAGCTTGGTCAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTATAAGAAGTTTGCATCATCATGGATTACGAGTGCAGTTTGAGAATAAACTTTCGCATCTGCTTGATTACCATATCcaa                                                             >  1:71788/1‑141 (MQ=255)

                                                                        gTCTTTTGTAGCTTGGTCAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGaa                                                                                               <  1:151090/106‑1 (MQ=255)

                                                                        gTCTTTTGTAGCTTGGTCAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGaa                                                                                               >  2:151090/1‑106 (MQ=255)

                                                                                 aGCTTGGTCAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCATATCCAACAACGCCAGt                                                   <  2:238015/141‑1 (MQ=255)

                                                                                             aTTCTTATCTAATAACACATCAATATAACTTAATTCATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCATATCCAACAACGCCAGTTGCTAAAACAcc                                       <  2:103928/141‑1 (MQ=255)

                                                                                                   aTCTAATAACACATCAATATAACTTAATTCATGTTATCAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGAATCTGCTTGATTCCCATATCCACCCACGCCAGTTGCTAAAACACCCACCAt                                 >  2:112211/1‑141 (MQ=255)

                                                                                                          aaCACATCAATATAACTTAATTCATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCATATCCAACAACGCCAGTTGCTAAAACACCTACCATTGCCGTa                          >  2:228243/1‑141 (MQ=255)

                                                                                                            cacaTCAATATAACTTAATTCATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCATATCCAACAACGCCAGTTGCTAAAACACCTACCATTGCCGTAGc                        >  1:272101/1‑141 (MQ=255)

                                                                                                               aTCAATATAACTTAATTCATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCATATCCAACAACGCCAGTTGCTAAAACACCTACCATTGCCGTAGctac                     >  2:21769/1‑141 (MQ=255)

                                                                                                               aTCAATATAACTTAATTCATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCATATCCAACAACGCCAGTTGCTAAAACACCTACCATTGCCGTAGctac                     >  2:346650/1‑141 (MQ=255)

                                                                                                               aTCAATATAACTTAATTCATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCATATCCAACAACGCCAGTTGCTAAAACACCTACCATTGCCGTAGctac                     >  2:346623/1‑141 (MQ=255)

                                                                                                                tCAATATAACTTAATTCATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCATATCCAACAACGCCAGTTGCTAAAACACCTACCATTGCCGTAGctact                    >  2:215510/1‑141 (MQ=255)

                                                                                                                      taACTTAATTCATGTTATAAGAAGTTTGCATCATCATGAAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGAtt                                                                        <  2:329633/83‑1 (MQ=255)

                                                                                                                      taACTTAATTCATGTTATAAGAAGTTTGCATCATCATGAAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGAtt                                                                        >  1:329633/1‑83 (MQ=255)

                                                                                                                                 aTGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCATATCCAACAACGCCAGTTGCTAAAACACCTACCATTGCCGTAGCTACTAAAACCTTTTTAAAttt   <  2:232740/141‑1 (MQ=255)

                                                                                                                                  tGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCATATCCAACAACGCCAGTTGCTAAAACACCTACCATTGCCGTAGCTACTAAAACCTTTTTAAATTTc  >  2:26831/1‑141 (MQ=255)

GTCTTGTTTAGCTTTGTTGATAATGTCTTTGATTGAATGTAGTCCTTTATCGGCGAAGTATGATCTTAAGTTGTCTTTTGTAGCTTGGTCAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTCTAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCATATCCAACAACGCCAGTTGCTAAAACACCTACCATTGCCGTAGCTACTAAAACCTTTTTAAATTTC  >  CP000730/462880‑463150

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