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
A2 F1 I1 R1	81	28.9	1316934	95.8%	1261622	113.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,661,308	T→C	R251R (CGT→CGC)	ynfF →	S‑ and N‑oxide reductase, A subunit, periplasmic

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,661,308	0	T	C	100.0%	121.9 / NA	33	R251R (CGT→CGC)	ynfF	S‑ and N‑oxide reductase, A subunit, periplasmic
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (15/18); total (15/18)

TCGGTGCCAATGATGGCAACAGCCCGGATGATATCGCCAATACGAAACTGGTCGTTATGTTCGGAAATAACCCGGCAGAAACGCGGATGAGCGGCGGTGGTGTCACTTACTACGTCGAGCAAGCCCGCGAACGTTCAAACGCACGCATGATCGTCATCGATCCACGTTATAACGACACTGCTGCCGGGCGTGAAGATGAATGGCTGCCCATTCGCCCTGGCACCGATGGCGCACTGGCCTGTGCGATTGCCTGGGTACTGATTACT  >  NC_000913/1661175‑1661440

tCGGTGCCAATGATGGCAACAGCCCGGATGATATCGCCAATACGAAACTGGTCGTTATGTTGGGAAATAACCCGGCAGAAACGCGGATGAGCGGCGGTGGTGTCACTTACTACGTCGAGCAAGCCCGCGAACGCTCaaa                                                                                                                                 >  2:133338/1‑139 (MQ=255)

tCGGTGCCAATGATGGCAACAGCCCGGATGATATCGCCAATACGAAACTGGTCGTTATGTTCGGAAATAACCCGGCAGAAACGCGGATGAGCGGCGGTGGTGTCACTTACTACGTCGAGCAAGCCCGCGAACGCTCaaa                                                                                                                                 >  2:200029/1‑139 (MQ=255)

 cGGTGCCAATGATGGCAACAGCCCGGATGATATCGCCAATACGAAACTGGTCGTTATGTTCGGAAATAACCCGGCAGAAACGCGGATGAGCGGCGGTGGTGTCACTTACTACGTCGAGCAAGCCCGCGAACGCTCAAac                                                                                                                                >  2:305291/1‑139 (MQ=255)

  ggTGCCAATGATGGCAACAGCCCGGATGATATCGCCAATACGAAACTGGTCGTTATGTTCGGAAATAACCCGGCAGAAACGCGGATGAGCGGCGGTGGTGTCACTTACTACGTCGAGCAAGCCCGCGAACGCTCAAacg                                                                                                                               <  2:414337/139‑1 (MQ=255)

   gTGCCAATGATGGCAACAGCCCGGATGATATCGCCAATACGAAACTGGTCGTTATGTTCGGAAATAACCCGGCAGAAACGCGGATGAGCGGCGGTGGTGTCACTTACTACGTCGAGCAAGCCCGCGAACGCTCAAacgc                                                                                                                              <  2:573382/139‑1 (MQ=255)

    tGCTAATGATGGCAACAGCCCGGATGATATCGCCAATACGAAACTGGTCGTTATGTTCGGAAATAACCCGGCAGAAACGCGGATGCGCGGCGGTGGTGTCACTTACTACGTCGAGCAAGCCCGCGAACGCTCAAacgca                                                                                                                             <  1:582347/139‑1 (MQ=255)

     gCCAATGATGGCAACAGCCCGGATGATATCGCCAATACGAAACTGGTCGTTATGTTCGGAAATAACCCGGCAGAAACGCGGATGAGCGGCGGTGGTGTCACTTACTACGTCGAGCAAGCCCGCGAACGCTCAAacgcac                                                                                                                            >  1:78584/1‑139 (MQ=255)

                       ccGGATGATATCGCCAATACGAAACTGGTCGTTATGTTCGGAAATAACCCGGCAGAAACGCGGATGAGCGGCGGTGGTGTCACTTACTACGTCGAGCAAGCCCGCGAACGCTCAAACGCACGCATGATCGTCATCGATc                                                                                                          <  1:276528/139‑1 (MQ=255)

                          gatgatATCGCCAATACGAAACTGGTCGTTATGTTCGGAAATAACCCGGCAGAAACGCGGATGAGCGGCGGTGGTGTCACTTACTACGTCGAGCAAGCCCGCGAACGCTCAAACGCACGCATGATCGTCATCGATCCAc                                                                                                       >  1:444288/1‑139 (MQ=255)

                                    ccAATACGAAACTGGTCGTTATGTTCGGAAATAACCCGGCAGAAACGCGGATGAGCGGCGGTGGTGTCACTTACTACGTCGAGCAAGCCCGCGAACGCTCAAACGCACGCATGATCGTCATCGATCCACGTTATAACGa                                                                                             <  2:366745/139‑1 (MQ=255)

                                      aaTACGAAACTGGTCGTTATGTTCGGAAATAACCCGGCAGAAACGCGGATGAGCGGCGGTGGTGTCACTTACTACGTCGAGCAAGCCCGCGAACGCTCAAACGCACGCATGATCGTCATCGATCCACGTTATAACGaca                                                                                           <  2:530177/139‑1 (MQ=255)

                                                    cGTTATGTTCGGAAATAACCCGGCAGAAACGCGGATGAGCGGCGGTGGTGTCACTTACTACGTCGAGCAAGCCCGCGAACGCTCAAACGCACGCATGATCGTCATCGATCCACGTTATAACGACACTGCTGCCGGGCGt                                                                             <  2:78584/139‑1 (MQ=255)

                                                                          gCAGAAACGCGGATGAGCGGCGGTGGTGTCACTTACTACGTCGAGCAAGCCCGCGAACGCTCAAACGCACGCATGATCGTCATCGATCCAc                                                                                                       <  2:9788/91‑1 (MQ=255)

                                                                          gCAGAAACGCGGATGAGCGGCGGTGGTGTCACTTACTACGTCGAGCAAGCCCGCGAACGCTCAAACGCACGCATGATCGTCATCGATCCAc                                                                                                       >  1:9788/1‑91 (MQ=255)

                                                                          gCAGAAACGCGGATGAGCGGCGGTGGTGTCACTTACTACGTCGAGCAAGCCCGCGAACGCTCAAACGCACGCATGATCGTCATCGATCCACGTTATAACGACACTGCTGCCGGGCGTGAAGATGAATGGCTGCCCATTc                                                       >  2:614245/1‑139 (MQ=255)

                                                                             gAAACGCGGATGAGCGGCGGTGGTGTCACTTACTACGTCGAGCAAGCCCGCGAACGCTCAAACGCACGCATGATCGTCATCGATCCACGTTATAACGACACTGCTGCCGGGCGTGAAGATGAATGGCTGCCCATTCGcc                                                    <  2:65434/139‑1 (MQ=255)

                                                                                       tGAGCGGCGGTGGTGTCACTTACTACGTCGAGCAAGCCCGCGAACGCTCAAACGCACGCATGATCGTCATCGATCCACGTTATAACGACACTGCTGCCGGGCGTGAAGATGAATGGCTGCCCATTCGCCCTGGCACCGa                                          <  1:26794/139‑1 (MQ=255)

                                                                                            ggcggTGGTGTCACTTACTACGTCGAGCAAGCCCGCGAACGCTCAAACGCACGCATGATCGTCATCGATCCACGTTATAACGACACTGCTGCCGGGCGTGAAGATGAATGGCTGCCCATTCGCCCTGGCACCGATGgcg                                     >  1:231954/1‑139 (MQ=255)

                                                                                              cggTGGTGTCACTTACTACGTCGAGCAAGCCCGCGAACGCTCAAACGCACGCATGATCGTCATCGATCCACGTTATAACGACACTGCTGCCGGGCGTGAAGATGAATGGCTGCCCATTCGCCCTGGCACCGATGGCGCa                                   <  1:305291/139‑1 (MQ=255)

                                                                                              cggTGGTGTCACTTACTACGTCGAGCAAGCCCGCGAACGCTCAAACGCACGCATGATCGTCATCGATCCACGTTATAACGACACTGCTGCCGGGCGTGAAGATGAATGGCTGCCCATTCGCCCTGGCACCGATGGCGCa                                   <  1:200029/139‑1 (MQ=255)

                                                                                                gtggtgTCACTTACTACGTCGAGCAAGCCCGCGAACGCTCAAACGCACGCATGATCGTCATCGATCCACGTTATAACGACACTGCTGCCGGGCGTGAAGATGAATGGCTGCCCATTCGCCCTGGCACCGATGGCGCACt                                 >  1:14730/1‑139 (MQ=255)

                                                                                                           tactacGTCGAGCAAGCCCGCGAACGCTCAAACGCACGCATGATCGTCATCGATCCACGTTATAACGACACTGCTGCCGGGCGTGAAGATGAATGGCTGCCCATTCGCCCTGGCACCGATGGCGCACTGGCCTGTGCGa                      >  2:452196/1‑139 (MQ=255)

                                                                                                                cGTCGAGCAAGCCCGCGAACGCTCAAACGCACGCATGATCGTCATCGATCCACGTTATAACGACACTGCTGCCGGGCGTGAAGATGAATGGCTGCCCATTCGCCCTGGCACCGATGGCGCACTGGCCTGTGCGa                      >  2:191854/1‑134 (MQ=255)

                                                                                                                cGTCGAGCAAGCCCGCGAACGCTCAAACGCACGCATGATCGTCATCGATCCACGTTATAACGACACTGCTGCCGGGCGTGAAGATGAATGGCTGCCCATTCGCCCTGGCACCGATGGCGCACTGGCCTGTGCGa                      <  1:191854/134‑1 (MQ=255)

                                                                                                                 gTCGAGCAAGCCCGCGAACGCTCAAACGCACGCATGATCGTCATCGATCCACGTTATAACGACACTGCTGCCGGGCGTGAAGATGAATGGCTGCCCATTCGCCCTGGCACCGATGGCGCACTGGCCTGTGCGATTGCCt                <  1:133338/139‑1 (MQ=255)

                                                                                                                   cGAGCAAGCCCGCGAACGCTCAAACGCACGCATGATCGTCATCGATCCAc                                                                                                       <  1:355468/50‑1 (MQ=255)

                                                                                                                   cGAGCAAGCCCGCGAACGCTCAAACGCACGCATGATCGTCATCGATCCAc                                                                                                       >  2:355468/1‑50 (MQ=255)

                                                                                                                    gAGCAAGCCCGCGAACGCTCAAACGCACGCATGATCGTCATCGATCCACGTTATAACGACACTGCTGCCGGGCGTGAAGATGAATGGCTGCCCATTCGCCCTGGCACCGATGGCGCACTGGCCTGTGCGATTGCCTggg             >  1:220127/1‑139 (MQ=255)

                                                                                                                     aGCAAGCCCGCGAACGCTCAAACGCACGCATGATCGTCATCGATCCACGTTATAACGACACTGCTGCCGGGCGTGAAGATGAATGGCTGCCCATTCGCCCTGGCACCGATGGCGCACTGGCCTGTGCGATTGCCTGGGt            >  1:208788/1‑139 (MQ=255)

                                                                                                                     aGCAAGCCCGCGAACGCTCAAACGCACGCATGATCGTCATCGATCCACGTTATAACGACACTGCTGCCGGGCGTGAAGATGAATGGCTGCCCATTCGCCCTGGCACCGATGGCGCACTGGCCTGTGCGATTGCCTGGGt            >  2:23395/1‑139 (MQ=255)

                                                                                                                          gCCCGCGAACGCTCAAACGCACGCATGATCGTCATCGATCCACGTTATAACGACACTGCTGCCGGGCGTGAAGATGAATGGCTGCCCATTCGCCCTGGCACCGATGGCGCACTGGCCTGTGCGATTGCCTGGGTACTGa       <  1:614245/139‑1 (MQ=255)

                                                                                                                           cccGCGAACGCTCAAACGCACGCATGATCGTCATCGATCCACGTTATAACGACACTGCTGCCGGGCGTGAAGATGAATGGCTGCCCATTCGCCCTGGCACCGATGGCGCACTGGCCTGTGCGATTGCCTGGGTACTGAt      <  2:444288/139‑1 (MQ=255)

                                                                                                                               cgAACGCTCAAACGCACGCATGATCGTCATCGATCCACGTTATAACGACACTGCTGCCGGGCGTGAAGATGAATGGCTGCCCATTCGCCCTGGCACCGATGGCGCACTGGCCTGTGCGATTGCCTGGGTACTGATTACt  <  2:208788/139‑1 (MQ=255)

TCGGTGCCAATGATGGCAACAGCCCGGATGATATCGCCAATACGAAACTGGTCGTTATGTTCGGAAATAACCCGGCAGAAACGCGGATGAGCGGCGGTGGTGTCACTTACTACGTCGAGCAAGCCCGCGAACGTTCAAACGCACGCATGATCGTCATCGATCCACGTTATAACGACACTGCTGCCGGGCGTGAAGATGAATGGCTGCCCATTCGCCCTGGCACCGATGGCGCACTGGCCTGTGCGATTGCCTGGGTACTGATTACT  >  NC_000913/1661175‑1661440

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 23 ≤` `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