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
A3 F1 I2 R1	777	59.2	2955938	92.5%	2734242	106.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,300,619	T→C	Y712C (TAC→TGC)	napA ←	nitrate reductase, periplasmic, large subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,300,619	0	T	C	100.0%	141.6 / NA	40	Y712C (TAC→TGC)	napA	nitrate reductase, periplasmic, large subunit
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (20/20); total (20/20)

CGCTTTCGCATCCAGCGGGTGAATAAACAGGACCGCTTCCGGGAAGGCGCGGTGCAGTTCTGGTACACGGCGAGTCATACTGCCGGTGTGCCAGTGCTCCAGAACGCGTCCGGTAGAGAGCCACAGGTCGTACTCTTCATCCGGTGCTTCCGCCGCCGGTTCGAATGGCAGTGCGAAGATCACCGCTTTGCCATCCGGTTTACCGTAGAACTTATAGCCTTCGCCCGCTTTCACGTACGGGTCGTTACCTTCGCTGTAACGCCAC  >  NC_000913/2300489‑2300753

cgcTTTCGCATCCAGCGGGTGAATAAACAGGACCGCTTCCGGGAAGGCGCGGTGCAGTTCTGGTACACGGCGAGTCATACTGCCGGTGTGCCAGTGCTCCAGAACGCGTCCGGTAGAGAGCCACAGGTCGCACTCTTCa                                                                                                                                <  1:240354/139‑1 (MQ=255)

     tCGCATCCAGCGGGTGAATAAACAGGACCGCTTCCGGGAAGGCGCGGTGCAGTTCTGGTACACGGCGAGTCATACTGCCGGTGTGCCAGTGCTCCAGAACGCGTCCGGTAGAGAGACACAGGTCGCACTCTTCATCCgg                                                                                                                           >  2:484845/1‑139 (MQ=255)

                             ggACCGCTTCCGGGAAGGCGCGGTGCAGTTCTGGTACACGGCGAGTCATACTGCCGGTGTGCCAGTGCTCCAGAACGCGTCCGGTAGAGAGCCACAGGTCGCACTCTTCATCCGGTGCTTCCGCCGCCGGTTCGAATgg                                                                                                   <  1:1055512/139‑1 (MQ=255)

                               aCCGCTTCCGGGAAGGCGCGGTGCAGTTCTGGTACACGGCGAGTCATACTGCCGGTGTGCCAGTGCTCCAGAACGCGTCCGGTAGAGAGCCACAGGTCGCACTCTTCATCCGGTGCTTCCGCCGCCGGTTCGAATGGCa                                                                                                 >  1:772816/1‑139 (MQ=255)

                                   cTTCCGGGAAGGCGCGGTGCAGTTCTGGTACACGGCGAGTCATACTGCCGGTGTGCCAGTGCTCCAGAACGCGTCCGGTAGAGAGCCACAGGTCGCACTCTTCATCCGGTGCTTCCGCCGCCGGTTCGAATgg                                                                                                   <  2:961804/133‑1 (MQ=255)

                                   cTTCCGGGAAGGCGCGGTGCAGTTCTGGTACACGGCGAGTCATACTGCCGGTGTGCCAGTGCTCCAGAACGCGTCCGGTAGAGAGCCACAGGTCGCACTCTTCATCCGGTGCTTCCGCCGCCGGTTCGAATGGCAGTGc                                                                                             >  2:1251589/1‑139 (MQ=255)

                                   cTTCCGGAAAGGCGCGGTGCAGTTCTGGTACACGGCGAGTCATACTGCCGGTGTGCCAGTGCCCCAGAACGCGTCCGGTAGAGAGCCACAGGTCGCACTCTTCATCCGGTGCTTCCGCCGCCGGTTCGAATgg                                                                                                   >  1:961804/1‑133 (MQ=255)

                                    ttCCGGGAAGGCGCGGTGCAGTTCTGGTACACGGCGAGTCATACTGCCGGTGTGCCAGTGCTCCAGAACGCGTCCGGTAGAGAGCCACAGGTCGCACTCTTCATCCGGTGCTTCCGCCGCCGGTTCGAATGGCAGTGCg                                                                                            <  1:640811/139‑1 (MQ=255)

                                      ccGGGAAGGCGCGGTGCAGTTCTGGTACACGGCGAGTCATACTGCCGGTGTGCCAGTGCTCCAGAACGCGTCCGGTAGAGAGCCACAGGTCGCACTCTTCATCCGGTGCTTCCGCCGCCGGTTCGAATGGCAGTGCGaa                                                                                          >  1:290454/1‑139 (MQ=255)

                                              gcgcGGTGCAGTTCTGGTACACGGCGAGTCATACTGCCGGTGTGCCAGTGCTCCAGAACGCGTCCGGTAGAGAGCCACAGGTCGCACTCTTCATCCGGTGCTTCCGCCGCCGGTTCGAATGGCAGTGCGAAGATCACCg                                                                                  >  2:1023486/1‑139 (MQ=255)

                                              gcgcGGTGCAGTTCTGGTACACGGCGAGTCATACTGCCGGTGTGCCAGTGCTCCAGAACGCGTCCGGTAGAGAGCCACAGGTCGCACTCTTCATCCGGTGCTTCCGCCGCCGGTTCGAATGGCAGTGCGAAGATCACCg                                                                                  >  2:192620/1‑139 (MQ=255)

                                                gcgGTGCAGTTCTGGTACACGGCGAGTCATACTGCCGGTGTGCCAGTGCTCCAGAACGCGTCCGGTAGAGAGCCACAGGTCGCACTCGTCATCCGGTGCTTCCGCCGCCGGTTCGAATGGCAGTGCGAAGATCACCGCt                                                                                >  1:983171/1‑139 (MQ=255)

                                                        gTTCTGGTACACGGCGAGTCATACTGCCGGTGTGCCAGTGCTCCAGAACGCGTCCGGTAGAGAGCCACAGGTCGCACTCTTCATCCGGTGCTTCCGCCGCCGGTTCGAATGGCAGTGCGAAGATCACCGCTTTGCCATc                                                                        <  2:146236/139‑1 (MQ=255)

                                                              gTACACGGCGAGTCATACTGCCGGTGTGCCAGTGCTCCAGAACGCGTCCGGTAGAGAGCCACAGGTCGCACTCTTCATCCGGTGCTTCCGCCGCCGGTTCGAATGGCAGTGCGAAGATCACCGCTTTGCCATCCGGttt                                                                  >  1:229445/1‑139 (MQ=255)

                                                              gTACACGGCGAGTCATACTGCCGGTGTGCCAGTGCTCCAGAACGCGTCCGGTAGAGAGCCACAGGTCGCACTCTTCATCCGGTGCTTCCGCCGCCGGTTCGAATGGCAGTGCGAAGATCACCGCTTTGCCATCCGGttt                                                                  >  2:530899/1‑139 (MQ=255)

                                                              gTACACGGCGAGTCATACTGCCGGTGTGCCAGTGCTCCAGAACGCGTCCGGTAGAGAGCCACAGGTCGCACTCTTCATCCGGTGCTTCCGCCGCCGGTTCGAATGGCAGTGCGAAGATCACCGCTTTGCCATCCGGttt                                                                  >  1:977261/1‑139 (MQ=255)

                                                              gTACACGGCGAGTCATACTGCCGGTGTGCCAGTGCTCCAGAACGCGTCCGGTAGAGAGCCACAGGTCGCACTCTTCATCCGGTGCTTCCGCCGCCGGTTCGAATGGCAGTGCGAAGATCACCGCTTTGCCATCCGGttt                                                                  >  1:1329664/1‑139 (MQ=255)

                                                                   cGGCGAGTCATACTGCCGGTGTGCCAGTGCTCCAGAACGCGTCCGGTAGAGAGCCACAGGTCGCACTCTTCATCCGGTGCTTCCGCCGCCGGTTCGAATGGCAGTGCGAAGATCACCGCTTTGCCATCCGGTTTACCGt                                                             >  1:850599/1‑139 (MQ=255)

                                                                    ggCGAGTCATACTGCCGGTGTGCCAGTGCTCCAGAACGCGTCCGGTAGAGAGCCACAGGTCGCACTCTTCATCCGGTGCTTCCGCCGCCGGTTCGAATGGCAGTGCGAAGATCACCGCTTTGCCATCCGGTTTACCGTa                                                            <  1:1246772/139‑1 (MQ=255)

                                                                    ggCGAGTCATACTGCCGGTGTGCCAGTGCTCCAGAACGCGTCCGGTAGAGAGCCACAGGTCGCACTCTTCATCCGGTGCTTCCGCCGCCGGTTCGAATAGCAGTGCGAAGATCACCGCTTTGCCATCCGGTTTACCGTa                                                            <  1:1311798/139‑1 (MQ=255)

                                                                     gCGAGTCATACTGCCGGTGTGCCAGTGCTCCAGAACGCGTCCGGTAGAGAGCCACAGGTCGCACTCTTCATCCGGTGCTTCCGCCGCCGGTTCGAATGGCAGTGCGAAGATCACCGCTTTGCCATCCGGTTTACCGTAg                                                           <  2:452260/139‑1 (MQ=255)

                                                                     gCGAGTCATACTGCCGGTGTGCCAGTGCTCCAGAACGCGTCCGGTAGAGAGCCACAGGTCGCACTCTTCATCCGGTGCTTCCGCCGCCGGTTCGAATGGCAGTGCGAAGATCACCGCTTTGCCATCCGGTTTACCGTAg                                                           <  1:1023486/139‑1 (MQ=255)

                                                                     gCGAGTCATACTGCCGGTGTGCCAGTGCTCCAGAACGCGTCCGGTAGAGAGCCACAGGTCGCACTCTTCATCCGGTGCTTCCGCCGCCGGTTCGAATGGCAGTGCGAAGATCACCGCTTTGCCATCCGGTTTACCGTAg                                                           <  2:1329664/139‑1 (MQ=255)

                                                                      cGAGTCATACTGCCGGTGTGCCAGTGCTCCAGAACGCGTCCGGTAGAGAGCCACAGGTCGCACTCTTCATCCGGTGCTTCCGCCGCCGGTTCGAATGGCAGTGCGAAGATCACCGCTTTGCCa                                                                          <  2:142593/123‑1 (MQ=255)

                                                                      cGAGTCATACTGCCGGTGTGCCAGTGCTCCAGAACGCGTCCGGTAGAGAGCCACAGGTCGCACTCTTCATCCGGTGCTTCCGCCGCCGGTTCGAATGGCAGTGCGAAGATCACCGCTTTGCCa                                                                          >  1:142593/1‑123 (MQ=255)

                                                                                      tgtgCCAGTGCTCCAGAACGCGTCCGGTAGAGAGCCACAGGTCGCACTCTTCATCCGGTGCTTCCGCCGCCGGTTCGAATGGCAGTGCGAAGATCACCGCTTTGCCATCCGGTTTACCGTAGAACTTATAGCCTTCGcc                                          <  1:1251589/139‑1 (MQ=255)

                                                                                                cTCCAGAACGCGTCCGGTAGAGAGCCACAGGTCGCACTCTTCATCCGGTGCTTCCGCCGCCGGTTCGAATGGCAGTGCGAAGATCACCGCTTTGCCATCCGGTTTACCGTAGAACTTATAGCCTTCGCCCGCTTTCACg                                >  2:1156623/1‑139 (MQ=255)

                                                                                                cTCCAGAACGCGTCCGGTAGAGAGCCACAGGTCGCACTCTTCATCCGGTGCTTCCGCCGCCGGTTCGAATGGCAGTGCGAAGATCACCGCTTTGCCATCCGGTTTACCGTAGAACTTATAGCCTTCGCCCGCTTTCACg                                >  2:1407115/1‑139 (MQ=255)

                                                                                                  ccAGAACGCGTCCGGTAGAGAGCCACAGGTCGCACTCTTCATCCGGTGCTTCCGCCGCCGGTTCGAATGGCAGTGCGAAGAt                                                                                       <  1:670671/82‑1 (MQ=255)

                                                                                                  ccAGAACGCGTCCGGTAGAGAGCCACAGGTCGCACTCTTCATCCGGTGCTTCCGCCGCCGGTTCGAATGGCAGTGCGAAGAt                                                                                       >  2:670671/1‑82 (MQ=255)

                                                                                                    aGAACGCGTCCGGTAGAGAGCCACAGGTCGCACTCTTCATCCGGTGCTTCCGCCGCCGGTTCGAATGGCAGTGCGAAGATCACCGCTTAGCCATCCGGTTTACCGTAGAACTTATAGCCTTCGCCCGCTTTCACGTACg                            >  1:416192/1‑139 (MQ=255)

                                                                                                     gAACGCGTCCGGTAGAGAGCCACAGGTCGCACTCTTCATCCGGTGCTTCCGCCGCCGGTTCGAATGGCAGTGCGAAGATCACCGCTTTGCCATCCGGTTTACCGTAGAACTTATAGCCTTCGCCCGCTTTCACGTACgg                           <  2:159615/139‑1 (MQ=255)

                                                                                                      aaCGCGTCCGGTAGAGAGCCACAGGTCGCACTCTTCATCCGGTGCTTCCGCCGCCGGt                                                                                                           >  1:813809/1‑58 (MQ=255)

                                                                                                      aaCGCGTCCGGTAGAGAGCCACAGGTCGCACTCTTCATCCGGTGCTTCCGCCGCCGGt                                                                                                           <  2:813809/58‑1 (MQ=255)

                                                                                                             ccGGTAGAGAGCCACAGGTCGCACTCTTCATCCGGTGCTTCCGCCGCCGGTTCGAATGGCAGTGCGAAGATCACCGCTTTGCCATCCGGTTTACCGTAGAACTTATAGCCTTCGCCCGCTTTCACGTACGGGTCGTTAc                   <  1:192620/139‑1 (MQ=255)

                                                                                                                 tAGAGAGCCACAGGTCGCACTCTTCATCCGGTGCTTCCGCCGCCGGTTCGAATGGCAGTGCGAAGATCACCGCTTTGCCATCCGGTTTACCGTAGAACTTATAGCCTTCGCCCGCTTTCACGTACGGGTCGTTACCTTc               <  2:416192/139‑1 (MQ=255)

                                                                                                                       gCCACAGGTCGCACTCTTCATCCGGTGCTTCCGCCGCCGGTTCg                                                                                                        <  1:632712/44‑1 (MQ=255)

                                                                                                                       gCCACAGGTCGCACTCTTCATCCGGTGCTTCCGCCGCCGGTTCg                                                                                                        >  2:632712/1‑44 (MQ=255)

                                                                                                                             ggTCGCACTCTTCATCCGGTGCTTCCGCCGCCGGTTCGAATGGCAGTGCGAAGATCACCGCTTTGCCATCCGGTTTACCGTAGAACTTATAGCCTTCGCCCGCTTTCACGTACGGGTCGTTACCTTCGCTGTAACGCCa   <  1:1407115/139‑1 (MQ=255)

                                                                                                                              gTCGCACTCTTCATCCGGTGCTTCCGCCGCCGGTTCGAATGGCAGTGCGAAGATCACCGCTTTGCCATCCGGTTTACCGTAGAACTTATAGCCTTCGCCCGCTTTCACGTACGGGTCGTTACCTTCGCTGTAACGCCAc  <  1:484845/139‑1 (MQ=255)

CGCTTTCGCATCCAGCGGGTGAATAAACAGGACCGCTTCCGGGAAGGCGCGGTGCAGTTCTGGTACACGGCGAGTCATACTGCCGGTGTGCCAGTGCTCCAGAACGCGTCCGGTAGAGAGCCACAGGTCGTACTCTTCATCCGGTGCTTCCGCCGCCGGTTCGAATGGCAGTGCGAAGATCACCGCTTTGCCATCCGGTTTACCGTAGAACTTATAGCCTTCGCCCGCTTTCACGTACGGGTCGTTACCTTCGCTGTAACGCCAC  >  NC_000913/2300489‑2300753

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A