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
A8 F28 I1 R1	95	36.3	1231394	98.7%	1215385	138.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,199,794	C→T	R338H (CGT→CAT)	intE ←	e14 prophage; putative integrase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,199,794	0	C	T	100.0%	129.6 / NA	37	R338H (CGT→CAT)	intE	e14 prophage; putative integrase
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (18/19); total (18/19)

TGGCGTTGAGATGCTTAAAGGTTCACAACGCTACTTTGCTCCATCCTTTACCTCGATCATCATGATAACGATCGGTTTGTTGTTGTGTTTTATGACCAAGTAGTTTTTGTGTGTCTAACCCCTGTTCTTTATACAGACGTTCAGATAAAGACCTTTGCTCATGGAATGTCGCAGGTGAACCCTCTCCCCAGTCAATTCTTGCTAAATCTCTCGCTTTACTAAAATTCATCGTCAATGTATTGGCTTTAACCTGCGCTCCGCGCTCTGCT  >  NC_000913/1199657‑1199925

tgGCGTTGAGATGCTTAAAGGTTCACAACGCTACTTTGCTCCATCCTTTACCTCGATCATCATGATAACGATCGGTTTGTTGTTGTGTTTTATGACCAAGTAGTTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGt                                                                                                                                   >  2:462251/1‑140 (MQ=255)

tgGCGTTGAGATGCTTAAAGGTTCACAACGCTACTTTGCTCCATCCTTTACCTCGATCATCATGATAACGATCGGTTTGTTGTTGTGTTTTATGACCAAGTAGTTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGt                                                                                                                                   >  1:393444/1‑140 (MQ=255)

 ggCGTTGAGATGCTTAAAGGTTCACAACGCTACTTTGCTCCATCCTTTACCTCGATCATCATGATAACGATCGGTTTGTTGTTGTGTTTTATGACCAAGTAGTTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGtt                                                                                                                                  <  2:116674/140‑1 (MQ=255)

          aTGCTTAAAGGTTCACAACGCTACTTTGCTCCATCCTTTACCTCGATCATCATGATAACGATCGGTTTGTTGTTGTGTTTTATGACCAAGTAGTTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGtt                                                                                                                                  <  2:592046/131‑1 (MQ=255)

          aTGCTTAAAGGTTCACAACGCTACTTTGCTCCATCCTTTACCTCGATCATCATGATAACGATCGGTTTGTTGTTGTGTTTTATGACCAAGTAGTTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGtt                                                                                                                                  >  1:592046/1‑131 (MQ=255)

             cTTAAAGGTTCACAACGCTACTTTGCTCCATCCTTTACCTCGATCATCATGATAACGATCGGTTTGTTGTTGTGTTTTATGACCAAGTAGTTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGTTTAGATAAAGAcc                                                                                                                      >  1:58062/1‑140 (MQ=255)

             cTTAAAGGTTCACAACGCTACTTTGCTCCATCCTTTACCTCGATCATCATGATAACGATCGGTTTGTTGTTGTGTTTTATGACCAAGTAGTTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGAcc                                                                                                                      >  1:137028/1‑140 (MQ=255)

             cTTAAAGGTTCACAACGCTACTTTGCTCCATCCTTTACCTCGATCATCATGATAACGATCGGTTTGTTGTTGTGTTTTATGACCAAGTAGTTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGAcc                                                                                                                      <  2:306748/140‑1 (MQ=255)

                  aGGTTCACAACGCTACTTTGCTCCATCCTTTACCTCGATCATCATGATAACGATCGGTTTGTTGTTGTGTTTTATGACCAAGTAGTTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGACCTTTGc                                                                                                                 <  1:549430/140‑1 (MQ=255)

                     ttCACAACGCTACTTTGCTCCATCCTTTACCTCGATCATCATGATAACGATCGGTTTGTTGTTGTGTTTTATGACCAAGTAGTTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGACCTTTGCTCa                                                                                                              <  2:393444/140‑1 (MQ=255)

                       cacaACGCTACTTTGCTCCATCCTTTACCTCGATCATCATGATAACGATCGGTTTGTTGTTGTGTTTTATGACCAAGTAGTTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGAcc                                                                                                                      >  1:400442/1‑130 (MQ=255)

                       cacaACGCTACTTTGCTCCATCCTTTACCTCGATCATCATGATAACGATCGGTTTGTTGTTGTGTTTTATGACCAAGTAGTTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGAcc                                                                                                                      <  2:400442/130‑1 (MQ=255)

                          aaCGCTACTTTGCTCCATCCTTTACCTCGATCATCATGATAACGATCGGTTTGTTGTTGTGTTTTATGACCAAGTAGTTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGACCTTTGCTCATGGaa                                                                                                         <  1:462251/140‑1 (MQ=255)

                                                      gATCATCATGATAACGATCGGTTTGTTGTTGTGTTTTATGACCAAGTAGTTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGACCTTTGCTCATGGAATGTCGCAGGTGAACCCTCTCCCCAGTCa                                                                             >  1:19306/1‑140 (MQ=255)

                                                               gATAACGATCGGTTTGTTGTTGTGTTTTATGACCAAGTAGTTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGACCTTTGCTCATGGAATGTCGCAGGTGAACCCTCTCCCCAGTCAATTCTTGCt                                                                    <  2:137028/140‑1 (MQ=255)

                                                                  aaCGATCGGTTTGTTGTTGTGTTTTATGACCAAGTAGTTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGACCTTTGCTCATGGAATGTCGCAGGTGAACCCTCTCCCCAGTCAATTCTTGCTaaa                                                                 >  1:69278/1‑140 (MQ=255)

                                                                    cGATCGGTTTGTTGTTGTGTTTTATGACCAAGTAGTTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGACCTTTGCTCATGGAATGTCGCAGGTGAACCCTCTCCCCAGTCAATTCTTGCTAAAtc                                                               >  2:105030/1‑140 (MQ=255)

                                                                      aTCGGTTTGTTGTTGTGTTTTATGACCAAGTAGTTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGACCTTTGCTCATGGAATGTCGCAGGTGAACCCTCTCCCCAGTCAATTCTTGCTAAAtctc                                                             >  2:55603/1‑140 (MQ=255)

                                                                      aTCGGTTTGTTGTTGTGTTTTATGACCAAGTAGTTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGACCTTTGCTCATGGAATGTCGCAGGTGAACCCTCTCCCCAGTCAATTCTTGCTAAAtctc                                                             >  1:326381/1‑140 (MQ=255)

                                                                         ggTTTGTTGTTGTGTTTTATGACCAAGTAGTTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGACCTTTGCTCATGGAATGTCGCAGGTGAACCCTCTCCCCAGTCAATTCTTGCTAAATCTCTCg                                                          >  2:536651/1‑140 (MQ=255)

                                                                          gTTTGTTGTTGTGTTTTATGACCAAGTAGTTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGACCTTTGCTCATGGAATGTCGCAGGTGAACCCTCTCCCCAGTCAATTCTTGCTAAATCTCTCGc                                                         <  1:536651/140‑1 (MQ=255)

                                                                                        tttATGACCAAGTAGTTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGACCTTTGCTCATGGAATGTCGCAGGTGAACCCTCTCCCCAGTCAATTCTTGCTAAATCTCTCGCTTTACTAAAATTCa                                           <  1:55603/140‑1 (MQ=255)

                                                                                         ttATGACCAAGTAGTTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGACCTTTGCTCATGGAATGTCGCAGGTGAACCCTCTCCCCAGTCAATTCTTGCTAAATCTCTCGCTTTACTAAAATTCAt                                          <  2:87718/140‑1 (MQ=255)

                                                                                            tGACCAAGTAGTTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGACCTTTGCTCATGGAATGTCGCAGGTGAACCCTCTCCCCAGTCAATTCTTGCTAAATCTCTCGCTTTACTAAAATTCATCGt                                       <  2:228244/140‑1 (MQ=255)

                                                                                               ccAAGTAGTTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGACCTTTGCTCATGGAATGTCGCAGGTGAACCCTCTCCCCAGTCAATTCTTGCTAAATCTCTCGCTTTACTAAAATTCATCGTCaa                                    >  2:322721/1‑140 (MQ=255)

                                                                                                 aaGTAGTTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGACCTTTGCTCATGGAATGTCGCAGGTGAACCCTCTCCCCAGTCAATTCTTGCTAAATCTCTCGCTTTACTAAAATTCATCGTCAATg                                  >  1:75677/1‑140 (MQ=255)

                                                                                                   gtagtTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGACCTTTGCTCATGGAATGTCGCAGGTGAACCCTCTCCCCAGTCAATTCTTGCTAAATCTCTCGCTTTACTAAAATTCATCGTCAATGTa                                <  2:75677/140‑1 (MQ=255)

                                                                                                    tagtTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGACCTTTGCTCATGGAATGTCGCAGGTGAACCCTCTCCCCAGTCAATTCTTGCTAAATCTCTCGCTTTACTAAAATTCATCGTCAATGTAt                               <  1:402872/140‑1 (MQ=255)

                                                                                                    tagtTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGACCTTTGCTCATGGAATGTCGCAGGTGAACCCTCTCCCCAGTCAATTCTTGCTAAATCTCTCGCTTTACTAAAATTCATCGTCAATGTAt                               <  2:19306/140‑1 (MQ=255)

                                                                                                           tgtgtgTCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGACCTTTGCTCATGGAATGTCGCAGGTGAACCCTCTCCCCAGTCAATTCTTGCTAAATCTCTCGCTTTACTAAAATTCATCGTCAATGTATTGGCttt                        <  2:236441/140‑1 (MQ=255)

                                                                                                             tgtgtCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGACCTTTGCTCATGGAATGTCGCAGGTGAACCCTCTCCCCAGTCAATTCTTGCTAAATCTCTCGCTTTACTAAAATTCATCGTCAATGTATTGGCTTTaa                      >  2:478567/1‑140 (MQ=255)

                                                                                                              gtgtCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGACCTTTGCTCATGGAATGTCGCAGGTGAACCCTCTCCCCAGTCAATTCTTGCTAAATCTCTCGCTTTACTAAAATTCATCGTCAATGTATTGGCTTTAAc                     <  2:69278/140‑1 (MQ=255)

                                                                                                                gtCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGACCTTTGCTCATGGAATGTCGCAGGTGAACCCTCTCCCCAGTCAATTCTTGCTAAATCTCTCGCTTTACTAAAATTCATCGTCAATGTAt                               <  2:323044/128‑1 (MQ=255)

                                                                                                                gtCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGACCTTTGCTCATGGAATGTCGCAGGTGAACCCTCTCCCCAGTCAATTCTTGCTAAATCTCTCGCTTTACTAAAATTCATCGTCAATGTAt                               >  1:323044/1‑128 (MQ=255)

                                                                                                                 tCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGACCTTTGCTCATGGAATGTCGCAGGTGAACCCTCTCCCCAGTCAATTCTTGCTAAATCTCTCGCTTTACTAAAATTCATCGTCAATGTATTGGCTTTAACCTg                  >  2:77981/1‑140 (MQ=255)

                                                                                                                            ttCTTTATACAGATGTTCAGATAAAGACCTTTGCTCATGGAATGTCGCAGGTGAACCCTCTCCCCAGTCAATTCTTGCTAAATCTCTCGCTTTACTAAAATTCATCGTCAATGTATTGGCTTTAACCTGCGCTCCGCGct       <  1:77981/140‑1 (MQ=255)

                                                                                                                                 tataCAGATGTTCAGATAAAGACCTTTGCTCATGGAATGTCGCAGGTGAACCCTCTCCCCAGTCAATTCTTGCTAAATCTCTCGCTTTACTAAAATTCATCGTCAATGTATTGGCTTTAACCTGCGCTCCGCGCTCTGCt  >  1:83044/1‑140 (MQ=255)

TGGCGTTGAGATGCTTAAAGGTTCACAACGCTACTTTGCTCCATCCTTTACCTCGATCATCATGATAACGATCGGTTTGTTGTTGTGTTTTATGACCAAGTAGTTTTTGTGTGTCTAACCCCTGTTCTTTATACAGACGTTCAGATAAAGACCTTTGCTCATGGAATGTCGCAGGTGAACCCTCTCCCCAGTCAATTCTTGCTAAATCTCTCGCTTTACTAAAATTCATCGTCAATGTATTGGCTTTAACCTGCGCTCCGCGCTCTGCT  >  NC_000913/1199657‑1199925

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A