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 F71 I1 R1	31	24.1	564604	94.3%	532421	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	2,102,618	T→C	intergenic (‑78/+238)	USA300HOU_RS10625 ← / ← USA300HOU_RS10630	hypothetical protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,102,618	0	T	C	100.0%	98.8 / NA	31	intergenic (‑78/+238)	USA300HOU_RS10625/USA300HOU_RS10630	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (14/17); total (14/17)

ATTTGCTTTTGGATCTTCTACTAATTGAATAATGTTACGTTTTAATTTTGCCATTTTATAATACTCTCCTTATTTTCAAATAAAATAGAGGGGTTGTCCCCTCT‑TATGCTTCTACATTTATTGTTATAGTGTCACTCATATTACCAACATATGCTTTAACCGTGGCAATACCTTGTGCTTCCGCAGTGACTTGACCATCACTATTGATTGATACAATATTCGTTTGATCTGTTGTGTATTTCAATAACTTACTTTGATTAGATGGCTC  >  USA300TCH1516_ALE/2102487‑2102754

aTTTGCTTTTGGATCTTCTACTAATTGAATAATGTTACGTCTTCTTTCCTCCCTTTTATCAAGCACTCCTTATTTTCAAATAAAATAGAGTGGTTGCCCCCTCT‑TATGCTTCTACATTTATTGTTATAGTGCCACTCatat                                                                                                                                 >  2:201648/1‑141 (MQ=255)

      ttttGGATCTTCTACTAATTGAATAATGTTACGTTTTAATTTTGCCATTTTATAATACTCTCCTTATTTTCAAATAAAATAGAGGGGTTGTCCCCTCT‑TATGCTTCTACATTTATTGTTATAGTGCCACTCATATTACCaa                                                                                                                           <  2:1401/141‑1 (MQ=255)

               ttctACTAATTGAATAATGTTACGTTTTAATTTTGCCATTTTATAATACTCTCCTTATTTTCAAATAAAATAGAGGGGTTGTCCCCTCT‑TATGCTTCTACATTTATTGTTATAGTGCCACTCATATTACCAACATATGCtt                                                                                                                  <  1:66232/141‑1 (MQ=255)

                      aaTTGAATAATGTTACGTTTTAATTTTGCCATTTTATAATACTCTCCTTATTTTCAAATAAAATAGAGGGGTTGTCCCCTCT‑TCTGCTTCTACTTTGATTGTTATTGTGCCACTCATATTACCAACATATGCTTTAAACGt                                                                                                           >  1:53511/1‑141 (MQ=255)

                        ttGAATAATGTTACGTTTTAATTTTGCCATTTTATAATACTCTCCTTATTTTCAAATAAAATAGAGGGGTTGTCCCCTCT‑TATGCTTCTACATTTATTGTTATAGTGCCACTCATATTACCAACATATTCTTTAACCGTgg                                                                                                         >  2:119023/1‑141 (MQ=255)

                                 gTTACGTTTTAATTTTGCCATTTTATAATACTCTCCTTATTTTCAAATAAAATAGAGGGGTTGTCCCCTCT‑TATGCTTCTACATTTATTGTTATAGTGCCACTCATATTACCAACATATGCTTTAACCGTGGCAATACCtt                                                                                                <  1:91837/141‑1 (MQ=255)

                                     cGTTTTAATTTTGCCATTTTATAATACTCTCCTTATTTTCAAATAAAATAGAGGGGTTGTCCCCTCT‑TATGCTTCTACATTTATTGTTATAGTGCCACTCATATTACCCCCATATCCTATACACGTGGCAATACCTTGTGc                                                                                            <  1:282173/141‑1 (MQ=255)

                                       ttttAATTTTGCTATTTTATAATACTCTCCTTATTTTCAAATAAAATAGAGGGGTTGTCCCCTCT‑TATGCTTCTACATTTATTGTTATAGTGCCACTCATATTACCAACATATGCTTTAACCGTGGCAATACCTTGTGCtt                                                                                          <  2:152215/141‑1 (MQ=255)

                                         ttAATTTTGCCATTTTATAATACTCTCCTTATTTTCAAATAAAATGGAGGGGTTGTCCCCTCT‑TATGCTTCTACATTTATTGTTATAGTGCCACTCATATTACCTACATCTGCTTTAACCGTGGCACTACCTTGTGCttgc                                                                                        >  1:221595/1‑139 (MQ=255)

                                          tAATTTTGCCATTTTATAATACTCTCCTTATTTTCAAATAAAATAGAGGGGATGAAACGATA‑GATACTTCTACATTTATTTTTATAGTGCCACTCATATTACCAACATATGCTTTAACCGTGGAAATAACTTGGGTTTCCg                                                                                       >  1:179079/1‑141 (MQ=255)

                                           aaTTTTGCCATTTTATAATACTCTCCTTATTTTCAAATAAAATAGAGGGGTTGTCCCCTCT‑TATGCTTCTACATTTATTGTTATAGTGCCACTCATATTACCAACATATGCTTTAACCGTGGCAATACCTTGTGCTTCCGc                                                                                      >  1:10399/1‑141 (MQ=255)

                                            aTTTTGCCATTTTATAATACTCTCCTTATTTTCAAATAAAATAGAGGGGTTGTCCCCTCT‑TATGCTTCTACATTTATTGTTATAGTGCCACTCATATTACCAACATATGCTTTAACCGTGGCAATACCTTGTGCTTCCGCa                                                                                     >  1:183847/1‑141 (MQ=255)

                                                     ttttATAATACTCTCCTTATTTTCAAATAAAATAGAGGGGTTGTCCCCTCT‑TATGCTTCTACATTTATTGTTATAGTGCCACTCCTATTACAAACACATGCTTTAACCGTGGCAATACCTTGTGCTTCCGCAGTGACTTGa                                                                            <  1:268989/141‑1 (MQ=255)

                                                          taataCTCTCCTTATTTTCAAACAAAATAACGCGGGTGTGCCAGCTCGATAC‑GCATGAGTTATTGTTATAGTGCCATCCTCATTTCTAACATATGCTTTAACCGTGGCAATACCTTGTGCTTCCGCAGTGACTTGACCATc                                                                       <  1:277994/141‑1 (MQ=255)

                                                            ataCTCTCCTTATTTTCAAATAAAATAGAGGGGTTGTCCCCTCT‑TATGCTTCTACATTTATTGTTATAGTGCCACTCATATTACCAACATATGCTTTAACCGTGGCAATACCTTGTGCTTACGCAGTGACTTGACCATCAc                                                                     >  1:254304/1‑141 (MQ=255)

                                                                         tttCAAATAAAATAGAGGGGTTGTCCCCTCT‑TATGCTTCTACATTTATTGTTATAGTGCCACTCATATTACCAACATATGCTTTAACCGTGGCAATACCTTGTGCTTCCGCAGTGCCTTGACCATCACTATTGATTGATAc                                                        >  1:19390/1‑141 (MQ=255)

                                                                           tCAAATAAAATAGAGGGGTTGTCCCCTCT‑TATGCTTCTACATTTATTGTTATAGTGCCACTCATATTACCAACATATGCTTTAACCGTGGCAATACCTTGTGCTTCCGCAGTGACTTGACCATCACTATTGATTGATACaa                                                      >  1:95652/1‑141 (MQ=255)

                                                                              aataaaataGAGGGGTTGTCCCCTCT‑TATGCTTCTACATTTATTGTTATAGTGCCACTCATATTACCAACATATGCTTTAACCGTGGCAATACCTTGTGCTTCCGCAGTGACTTGACCATCACTATTGATTGATACAatat                                                   <  1:103965/141‑1 (MQ=255)

                                                                                      agagGGGTTGTCCCCTCT‑TATGCTTCTACATTTATTGTTATAGTGCCACTCATATTACCAACATATGCTTTAACCGTGGCAATACCTTGTGCTTCCGCAGTGACTTGACCATCACTATTGATTGATACAATATTCGTTTGa                                           <  1:234244/141‑1 (MQ=255)

                                                                                      agagGGGTTGTCCCCTAT‑TATGCTGCTACATTTATTGTTATAGTGCCACTCATATTACCAACATATGCTTTAACCGTGGCAATACCTTGTGCTTCCGCAGTGACTTGACCATCACTATTGATTGATACAATATTCGTTTGa                                           <  1:176245/141‑1 (MQ=255)

                                                                                       gagGGGTTGTCCCCTCT‑TATGCTTCTACATTTATTGTTATAGTGCCACTCATATTACCAACATATGCTTTAACCGTGGCAATACCTTGTGCTTCCGCAGTGACTTGACCATCACTATTGATTGATACAATATTCGTTTGAt                                          >  2:89048/1‑141 (MQ=255)

                                                                                        agGGGTTGTCCCCTCT‑TATGCTTCTAAAGTTATTGTTATAGTGCCACTCATATTACCAACGTATGCTTTAACCGTGGCAATACCTTGTGCTTCCGCAGTGACTTGACCATCACTATTGATTGATACAATATTCGTTTGATc                                         <  2:211129/141‑1 (MQ=255)

                                                                                            gTTGGCCCCTCT‑TATGCTTCTACATGTATTGTTATAGTGCCACTCAGATTACCAACATATGCTTTAACCGTGGCAATACCTTGTGCGTCCGCAGTGACTTGAACATCACTATTGATTGATACAATATTCGTTTGATCtgtt                                     <  1:268580/141‑1 (MQ=255)

                                                                                                tCCCCTCT‑TATGCTTCTACATTTATTGTTATAGTGCCACTCATATTACCAACATATGCTTTAACCGTGGCAATACCTTGTGCTTCCGCAGTGACTTGACCATCACTATTGATTGATACAATATTCGTTTGATCTGTTgtgt                                 >  1:7587/1‑141 (MQ=255)

                                                                                                tCCCCTCT‑TATGCTTCTACATTTATTGTTATAGTGCCACTCATATTACCAACATATGCTTTAACCGTGGCAATACCTTGTGCTTCCGCAGTGACTTGACCATCACTATTGATTGATACAATATTCGTTTGATCTGTTgtgt                                 >  2:263317/1‑141 (MQ=255)

                                                                                                tCCCCTCT‑TATGCTTCTACATTTATTGTTATAGTGCCACTCATATTACCAACATATGCTTTAACCGTGGCAATACCTTGTGCTTCCGCAGTGACTTGACCATCACTATTGATTGATACAATATTCGTTTGATCTGTTgtgt                                 >  1:139761/1‑141 (MQ=255)

                                                                                                       t‑tATGCTTCTACATTTATTGTTATAGTGCCACTCATATTACCAACATATGCTTTAACCGTGGCAATACCTTGTGCTTCCGCAGTGACTTGACCATCACTATTGATTGATACAATATTCGTTTGATCTGTTGTGTATTTCaa                          <  2:159218/141‑1 (MQ=255)

                                                                                                            gCTTCTACATTTATTGTTATAGGGCCACTCATATTACCAACATATGCTTTAACCGTGGCAATACCTTGTGCTTCCGCAGTGACTTGACCATCACTATTGATTGATACAATATTCGTTTGATCTGTTGTGTATTTCAATAac                      <  1:30600/141‑1 (MQ=255)

                                                                                                             cTTGTACATTTATTGTTATATTGCCACTCATATTACCAACATATGCTTTAACCGTGGCAATACCTTGTGCTTCCGCAGTGACTTGACCATCACTATTGATTGATACAATATTCGTTTGATCTGTTGTGTATTTCAATAact                     <  2:268137/141‑1 (MQ=255)

                                                                                                                     tttATTGTTATAGTGCCACTCATATTACCAACATATGCTTTAACCGTGGCAATACCTTGTGCTTCCGCAGTGACTTGACCATCACTATTGATTGATACAATATTCGTTTGATCTGTTGTGTATTTCAATAACTTACTTTGa             <  1:93716/141‑1 (MQ=255)

                                                                                                                                aGTGCCACTCATATTACCAACATATGCTTTAACCGTGGCAATACCTTGTGCTTCCGCAGTGACTTGACCATCACTATTGATTGATACAATATTCGTTTGATCTGTTGTGTATTTCAATAACTTACTTTGATTAGATGGctc  <  1:263317/141‑1 (MQ=255)

ATTTGCTTTTGGATCTTCTACTAATTGAATAATGTTACGTTTTAATTTTGCCATTTTATAATACTCTCCTTATTTTCAAATAAAATAGAGGGGTTGTCCCCTCT‑TATGCTTCTACATTTATTGTTATAGTGTCACTCATATTACCAACATATGCTTTAACCGTGGCAATACCTTGTGCTTCCGCAGTGACTTGACCATCACTATTGATTGATACAATATTCGTTTGATCTGTTGTGTATTTCAATAACTTACTTTGATTAGATGGCTC  >  USA300TCH1516_ALE/2102487‑2102754

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A