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
A7 F50 I2 R1	209	44.2	1360995	98.7%	1343302	150.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,646,854	C→T	intergenic (+117/+320)	flxA → / ← intK	Qin prophage; uncharacterized protein/pseudogene, integrase fragment, Qin prophage;Phage or Prophage Related

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,646,854	0	C	T	100.0%	121.2 / NA	32	intergenic (+117/+320)	flxA/intK	Qin prophage; uncharacterized protein/pseudogene, integrase fragment, Qin prophage;Phage or Prophage Related
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (16/16); total (16/16)

CCATTGATATTTACGTCTAAGTGACAGCCGTATTGTGGCCCTCATCGGGCCACTTTTCGCCATCAGCCTTTTCTTTAAAGACATATTATCTTTGTATCATTTCTGATAGTTAACATTACAAGATATAAGTAATGGACGCACTCCCAATTAGTCTATTTAAATCGCCACGAGTTTAACTGACAACCCATGATCAATTATGAATTGCAACTATTTCTGTAGTCACTTTTGTGGGGACAGTCCACAAAACTGCCAACTTCCGCTTCTTGCTCTTAGCGGACATT  >  NC_000913/1646718‑1646998

ccATTGATATTTACGTCTAAGTGACAGCCGTATTGTGGCCCTCATCGGGCCACTTTTCGCCATCAGCCTTTTCTTTAAAGACATATTATCTTTGTATCATTTCTGATAGTTAACATTACAAGATATAAGTAATGGATGCACTCCCAATTAg                                                                                                                                    <  2:88407/151‑1 (MQ=255)

 cATTGATATTTACGTCTAAGTGACAGCCGTATTGTGGCCCTCATCGGGCCACTTTTCGCCATCAGCCTTTTCTTTAAAGACATATTATCTTTGTATCATTTCTGATAGTTAACATTACAAGATATAAGTAATGGATGCACTCCCAATTAGt                                                                                                                                   >  2:32588/1‑151 (MQ=255)

      atatTTACGTCTAAGTGACAGCCGTATTGTGGCCCTCATCGGGCCACTTTTCGCCATCAGCCTTTTCTTTAAAGACATATTATCTTTGTATCATTTCTGATAGTTAACATTACAAGATATAAGTAATGGATGCACTCCCAATTAGTCTAtt                                                                                                                              <  1:59727/151‑1 (MQ=255)

         tttACGTCTAAGTGACAGCCGTATTGTGGCCCTCATCGGGCCACTTTTCGCCATCAGCCTTTTCTTTAAAGACATATTATCTTTGTATCATTTCTGATAGTTAACATTACAAGATATAAGTAATGGATGCACTCCCAATTAGTCTATTTa                                                                                                                            >  2:231998/1‑150 (MQ=255)

             cGTCTAAGTGACAGCCGTATTGTGGCCCTCATCGGGCCACTTTTCGCCATCAGCCTTTTCTTTAAAGACATATTATCTTTGTATCATTTCTGATAGTTAACATTACAAGATATAAGTAATGGATGCACTCCCAATTAGTCTATTTAAATCg                                                                                                                       <  1:372208/151‑1 (MQ=255)

             cGTCTAAGTGACAGCCGTATTGTGGCCCTCATCGGGCCACTTTTCGCCATCAGCCTTTTCTTTAAAGACATATTATCTTTGTATCATTTCTGATAGTTAACATTACAAGATATAAGTAATGGATGCACTCCCAATTAGTCTATTTAAATCg                                                                                                                       >  2:581290/1‑151 (MQ=255)

                  aaGTGACAGCCGTATTGTGGCCCTCATCGGGCCACTTTTCGCCATCAGCCTTTTCTTTAAAGACATATTATCTTTGTATCATTTCTGATAGTTAACATTACAAGATATAAGTAATGGATGCACTCCCAATTAGTCTATTTAAATCGCCACg                                                                                                                  <  2:259137/151‑1 (MQ=255)

                  aaGTGACAGCCGTATTGTGGCCCTCATCGGGCCACTTTTCGCCATCAGCCTTTTCTTTAAAGACATATTATCTTTGTATCATTTCTGATAGTTAACATTACAAGATATAAGTAATGGATGCACTCCCAATTAGTCTATTTAAATCGCCACg                                                                                                                  <  1:518159/151‑1 (MQ=255)

                      gACAGCCGTATTGTGGCCCTCATCGGGCCACTTTTCGCCATCAGCCTTTTCTTTAAAGACATATTATCTTTGTATCATTTCTGATAGTTAACATTACAAGATATAAGTAATGGATGCACTCCCAATTAGTCTATTTAAATCGCCACGAGt                                                                                                               <  1:379284/150‑1 (MQ=255)

                         aGCCGTATTGTGGCCCTCATCGGGCCACTTTTCGCCATCAGCCTTTTCTTTAAAGACATATTATCTTTGTATCATTTCTGATAGTTAACATTACAAGATATAAGTAATGGATGCACTCCCAATTAGTCTATTTAAATCGCCACGAGTTTaa                                                                                                           <  1:426294/151‑1 (MQ=255)

                             gTATTGTGGCCCTCATCGGGCCACTTTTCGCCATCAGCCTTTTCTTTAAAGACATATTATCTTTGTATCATTTCTGATAGTTAACATTACAAGATATAAGTAATGGATGCACTCCCAATTAGTCTATTTAAATCGCCACGAGTTTAACTg                                                                                                        >  2:399213/1‑150 (MQ=255)

                                              gggCCACTTTTCGCCATCAGCCTTTTCTTTAAAGACATATTATCTTTGTATCATTTCTGATAGTTAACATTACAAGATATAAGTAATGGATGCACTCCCAATTAGTCTATTTAAATCGCCACGAGTTTAACTGACAACCCATGATCAATTa                                                                                      <  2:346270/151‑1 (MQ=255)

                                               ggCCACTTTTCGCCATCAGCCTTTTCTTTAAAGACATATTATCTTTGTATCATTTCTGATAGTTAACATTACAAGATATAAGTAATGGATGCACTCCCAATTAGTCTATTTAAATCGCCACGAGTTTAACTGACAACCCATGATCAATTAt                                                                                     <  2:151197/151‑1 (MQ=255)

                                                      tttCGCCATCAGCCTTTTCTTTAAAGACATATTATCTTTGTATCATTTCTGATAGTTAACATTACAAGATATAAGTAATGGATGCACTCCCAATTAGTCTATTTAAATCGCCACGAGTTTAACTGACAACCCATGATCAATTATGAATTg                                                                               <  2:362257/150‑1 (MQ=255)

                                                          gCCATCAGCCTTTTCTTTAAAGACATATTATCTTTGTATCATTTCTGATAGTTAACATTACAAGATATAAGTAATGGATGCACTCCCAATTAGTCTATTTAAATCGCCACGAGTTTAACTGACAACCCATGATCAATTATGAATTGCAACt                                                                          <  1:22449/151‑1 (MQ=255)

                                                            cATCAGCCTTTTCTTTAAAGACATATTATCTTTGTATCATTTCTGATAGTTAACATTACAAGATATAAGTAATGGATGCACTCCCAATTAGTCTATTTAAATCGCCACGAGTTTAACTGACAACCCATGATCAATTATGAATTGCAACTAt                                                                        <  2:355867/151‑1 (MQ=255)

                                                            cATCAGCCTTTTCTTTAAAGACATATTATCTTTGTATCATTTCTGATAGTTAACATTACAAGATATAAGTAATGGATGCACTCCCAATTAGTCTATTTAAATCGCCACGAGTTTAACTGACAACCCATGATCAATTATGAATTGCAACTAt                                                                        >  2:3554/1‑151 (MQ=255)

                                                                         tttAAAGACATATTATCTTTGTATCATTTCTGATAGTTAACATTACAAGATATAAGTAATGGATGCACTCCCAATTAGTCTATTTAAATCGCCACGAGTTTAACTGACAACCCATGATCAATTATGAATTGCAACTATTTCTGTAGTCACt                                                           >  1:212249/1‑151 (MQ=255)

                                                                              aGACATATTATCTTTGTATCATTTCTGATAGTTAACATTACAAGATATAAGTAATGGATGCACTCCCAATTAGTCTATTTAAATCGCCACGAGTTTAACTGACAACCCATGATCAATTATGAATTGCAACTATTTCTGTAGTCACTTTtgc                                                      >  2:478941/1‑150 (MQ=255)

                                                                                    attatCTTTGTATCATTTCTGATAGTTAACATTACAAGATATAAGTAATGGATGCACTCCCAATTAGTCTATTTAAATCGCCACGAGTTTAACTGACAACCCATGATCAATTATGAATTGCAACTATTTCTGTAGTCACTTTTGTGGGGAc                                                <  1:31655/151‑1 (MQ=255)

                                                                                      tatCTTTGTATCATTTCTGATAGTTAACATTACAAGATATAAGTAATGGATGCACTCCCAATTAGTCTATTTAAATCGCCACGAGTTTAACTGACAACCCATGATCAATTATGAATTGCAACTATTTCTGTAGTCACTTTTGTGGGGAc                                                >  1:356606/1‑149 (MQ=255)

                                                                                          tttGTATCATTTCTGATAGTTAACATTACAAGATATAAGTAATGTATGCACTCCCAATTAGTCTATTTAAATCGCCACGAGTTTAACTGACAACCCATGATCAATTATGAATTGCAACTATTTCTGTAGTCACTTTTGTGGGGACAGTcc                                           >  2:242238/1‑150 (MQ=255)

                                                                                                 cATTTCTGATAGTTAACATTACAAGATATAAGTAATGGATGCACTCCCAATTAGTCTATTTAAATCGCCACGAGTTTAACTGACAACCCATGATCAATTATGAATTGCAACTATTTCTGTAGTCACTTTTGTGGGGACAGTCCACAAAACt                                   >  1:433987/1‑151 (MQ=255)

                                                                                                        gATAGTTAACATTACAAGATATAAGTAATGGATGCACTCCCAATTAGTCTATTTAAATCGCCACGAGTTTAACTGACAACCCATGATCAATTATGAATTGCAACTATTTCTGTAGTCACTTTTGTGGGGACAGTCCACAAAACTGCCAACt                            <  2:579002/151‑1 (MQ=255)

                                                                                                         aTAGTTAACATTACAAGATATAAGTAATGGATGCACTCCCAATTAGTCTATTTAAATCGCCACGAGTTTAACTGACAACCCATGATCAATTATGAATTGCAACTATTTCTGTAGTCACTTTTGTGGGGACAGTCCACAAAACTGCCAACtt                           >  1:92889/1‑151 (MQ=255)

                                                                                                            gTTAACATTACAAGATATAAGTAATGGATGCACTCCCAATTAGTCTATTTAAATCGCCACGAGTTTAACTGACAACCCATGATCAATTATGAATTGCAACTATTTCTGTAGTCACTTTTGTGGGGACAGTCCACAAAACTGCCAACTTcca                        <  2:394323/151‑2 (MQ=255)

                                                                                                            gTTAACATTACAAGATATAAGTAATGGATGCACTCCCAATTAGTCTATTTAAATCGCCACGAGTTTAACTGACAACCCATGATCAATTATGAATTGCAACTATTTCTGTAGTCACTTTTGTGGGGACAGTCCACAAAACTGCCAACTTcc                         >  2:76116/1‑150 (MQ=255)

                                                                                                                         gATATAAGTAATGGATGCACTCCCAATTAGTCTATTTAAATCGCCACGAGTTTAACTGACAACCCATGATCAATTATGAATTGCAACTATTTCTGTAGTCACTTTTGTGGGGACAGTCCACAAAACTGCCAACTTCCGCTTCTTGCTCtt            >  1:359100/1‑150 (MQ=255)

                                                                                                                              aaGTAATGGATGCACTCCCAATTAGTCTATTTAAATCGCCACGAGTTTAACTGACAACCCATGATCAATTATGAATTGCAACTATTTCTGTAGTCACTTTTGTGGGGACAGTCCACAAAACTGCCAACTTCCGCTTCTTGCTCTTAGCgg       >  2:224572/1‑150 (MQ=255)

                                                                                                                              aaGTAATGGATGCACTCCCAATTAGTCTATTTAAATCGCCACGAGTTTAACTGACAACCCATGATCAATTATGAATTGCAACTATTTCTGTAGTCACTTTTGTGGGGACAGTCCACAAAACTGCCAACTTCCGCTTCTTGCTCTTAGCgg       <  1:554201/150‑1 (MQ=255)

                                                                                                                                   aTGGATGCACTCCCAATTAGTCTATTTAAATCGCCACGAGTTTAACTGACAACCCATGATCAATTATGAATTGCAACTATTTCTGTAGTCACTTTTGTGGGGACAGTCCACAAAACTGCCAACTTCCGCTTCTTGCTCTTAGCGGACAtt  >  2:374629/1‑150 (MQ=255)

                                                                                                                                   aTGGATGCACTCCCAATTAGTCTATTTAAATCGCCACGAGTTTAACTGACAACCCATGATCAATTATGAATTGCAACTATTTCTGTAGTCACTTTTGTGGGGACAGTCCACAAAACTGCCAACTTCCGCTTCTTGCTCTTAGCGGACAtt  >  1:399960/1‑150 (MQ=255)

CCATTGATATTTACGTCTAAGTGACAGCCGTATTGTGGCCCTCATCGGGCCACTTTTCGCCATCAGCCTTTTCTTTAAAGACATATTATCTTTGTATCATTTCTGATAGTTAACATTACAAGATATAAGTAATGGACGCACTCCCAATTAGTCTATTTAAATCGCCACGAGTTTAACTGACAACCCATGATCAATTATGAATTGCAACTATTTCTGTAGTCACTTTTGTGGGGACAGTCCACAAAACTGCCAACTTCCGCTTCTTGCTCTTAGCGGACATT  >  NC_000913/1646718‑1646998

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A