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 F1 I1 R1	776	60.0	3074904	90.1%	2770488	104.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,744,740	C→T	G428G (GGC→GGT)	mdtK →	multidrug efflux system transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,744,740	0	C	T	100.0%	107.9 / NA	35	G428G (GGC→GGT)	mdtK	multidrug efflux system transporter
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (19/16); total (19/16)

ACGCGTTCCATTTTCTATATTACCTTTACGGCTTACTGGGTGCTGGGCTTGCCAAGCGGCTATATTCTGGCACTGACCGATCTGGTCGTTGAACCTATGGGGCCAGCAGGCTTCTGGATAGGCTTTATTATTGGCCTGACGTCGGCAGCCATTATGATGATGTTGCGTATGCGGTTCCTGCAACGTCTGCCGTCAGCCATCATTCTGCAACGAGCATCCCGCTAATAAAGACAAGGCGCAACCTTCACGGGTTGCGCCTGTATTTTTACG  >  NC_000913/1744606‑1744875

aCGCGTTCCATTTTCTATATTACCTTTACGGCTTACTGGGTGCTGGGCTTGCCAAGCGGCTATATTCTGGCACTGACCGATCTGGTCGTTGAACCTATGGGGCCAGCAGGCTTCTGGATAGGCTTTATTATTGGTCTGa                                                                                                                                     >  1:1338311/1‑139 (MQ=255)

        cATTTTCTATATTACCTTTACGGCTTACTGGGTGCTGGGCTTGCCAAGCGGCTATATTCTGGCACTGACCGATCTGGTCGTTGAACCTATGGGGCCAGCAGGCTTCTGGATAGGCTTTATTATTGGTCTGACGTCGGCa                                                                                                                             <  2:364760/139‑1 (MQ=255)

                    tACCTTTACGGCTTACTGGGTGCTGGGCTTGCCAAGCGGCTATATTCTGGCACTGACCGATCTGGTCGTTGAACCTATGGGGCCAGCAGGCTTCTGGATAGGCTTTATTATTGGTCTGACGTCGGCAGCCAt                                                                                                                        <  2:134041/132‑1 (MQ=255)

                    tACCTTTACGGCTTACTGGGTGCTGGGCTTGCCAAGCGGCTATATTCTGGCACTGACCGATCTGGTCGTTGAACCTATGGGGCCAGCAGGCTTCTGGATAGGCTTTATTATTGGTCTGACGTCGGCAGCCAt                                                                                                                        >  1:134041/1‑132 (MQ=255)

                         ttACGGCTTACTGGGTGCTGGGCTTGCCAAGCGGCTATATTCTGGCACTGACCGATCTGGTCGTTGAACCTATGGGGCCAGCAGGCTTCTGGATAGGCTTTATTATTGGTCTGACGTCGGCAGTCAt                                                                                                                        >  1:771347/1‑127 (MQ=255)

                         ttACGGCTTACTGGGTGCTGGGCTTGCCAAGCGGCTATATTCTGGCACTGACCGATCTGGTCGTTGAACCTATGGGGCCAGCAGGCTTCTGGATAGGCTTTATTATTGGTCTGACGTCGGCAGTCAt                                                                                                                        <  2:771347/127‑1 (MQ=255)

                           aCGGCTTACTGGGTGCTGGGCTTGCCAAGCGGCTATATTCTGGCACTGACCGATCTGGTCGTTGAACCTATGGGGCCAGCAGGCTTCTGGATAGGCTTTATTATTGGTCTGACGTCGGCAGCCATTATGATGATGTTGc                                                                                                          >  1:11651/1‑139 (MQ=255)

                                    tGGGTGCTGGGCTTGCCAAGCGGCTATATTCTGGCACTGACCGATCTGGTCGTTGAACCTATGGGGCCAGCAGGCTTCTGGATAGGCTTTATTATTGGTCGGTCGTCGGCAGCCATTATGATGATGTTGCGTATGCGGt                                                                                                 <  2:67268/139‑1 (MQ=255)

                                                  gCCAAGCGGCTATATTCTGGCACTGACCGATCTGGTCGTTGAACCTATGGGGCCAGCAGGCTTCTGGATAGGCTTTATTATTGGTCTGACGTCGGc                                                                                                                              >  1:38640/1‑96 (MQ=255)

                                                  gCCAAGCGGCTATATTCTGGCACTGACCGATCTGGTCGTTGAACCTATGGGGCCAGCAGGCTTCTGGATAGGCTTTATTATTGGTCTGACGTCGGc                                                                                                                              <  2:38640/96‑1 (MQ=255)

                                                            tataTTCTGGCACTGACCGATCTGGTCGTTGAACCTATGGGGCCAGCAGGCTTCTGGATAGGCTTTATTATTGGTCTGACGTCGGCAGCCATTATGATGATGTTGCGTATGCGGTTCCTGCAACGTCTGCCGTCAGCca                                                                         <  2:1338311/139‑1 (MQ=255)

                                                                     gCACTGACCGATCTGGTCGTTGAACCTCTGGGGCCAGCAGGCTTCTGGATAGGCTTTATTATTGGTCTGACGTCGGCAGCCATTATGATGATGTTGCGTATGCGGTTCCTGCAACGTCTGCCGTCAGCCATCATTCTGc                                                                >  1:410332/1‑139 (MQ=255)

                                                                     gCACTGACCGATCTGGTCGTTGAACCTATGGGGCCAGCAGGCTTCTGGATAGGCTTTATTATTGGTCTGACGTCGGCAGCCATTATGATGATGTTGCGTATGCGGTTCCTGCAACGTCTGCCGTCAGCCATCATTCTGc                                                                >  2:673211/1‑139 (MQ=255)

                                                                        cTGACCGATCTGGTCGTTGAACCTATGGGGCCAGCAGGCTTCTGGATAGGCTTTATTATTGGTCTGACGTCGGCAGCCATTATGATGATGTTGCGTATGCGGTTCCTGCAACGTCTGCCGTCAGCCATCATTCTGCAAc                                                             >  2:204259/1‑139 (MQ=255)

                                                                        cTGACCGATCTGGTCGTTGAACCTATGGGGCCAGCAGGCTTCTGGATAGGCTTTATTATTGGTCTGACGTCGGCAGCCATTATGATGATGTTGCGTATGCGGTTCCTGCAACGTCTGCCGTCAGCCATCATTCTGCAAc                                                             >  1:27370/1‑139 (MQ=255)

                                                                          gACCGATCTGGTCGTTGAACCTATGGGGCCAGCAGGCTTCTGGATAGGCTTTATTATTGGTCTGACGTCGGCAGCCATTATGATGATGTTGCGTATGCGGTTCCTGCAACGTCTGCCGTCAGCCATCATTCTGCAACg                                                            >  1:618592/1‑138 (MQ=255)

                                                                          gACCGATCTGGTCGTTGAACCTATGGGGCCAGCAGGCTTCTGGATAGGCTTTATTATTGGTCTGACGTCGGCAGCCATTATGATGATGTTGCGTATGCGGTTCCTGCAACGTCTGCCGTCAGCCATCATTCTGCAACg                                                            <  2:618592/138‑1 (MQ=255)

                                                                          gACCGATCTGGTCGTTGAACCTATGGGGCCAGCAGGCTTCTGGATAGGCTTTATTATTGGTCTGACGTCGGCAGCCATTATGATGATGTTGCGTATGCGGTTCCTGCAACGTCTGCCGTCAGCCATCATTCTGCAACGa                                                           >  1:1117605/1‑139 (MQ=255)

                                                                                  tGGTCGTTGAACCTATGGGGCCAGCAGGCTTCTGGATAGGCTTTATTATTGGTCTGACGTCGGCAGCCATTATGATGATGTTGCGTATGCGGTTCCTGCAACGTCTGCCGTCAGCCATCATTCTGCAACGAGCATCCCg                                                   <  1:673211/139‑1 (MQ=255)

                                                                                  tGGTCGTTGAACCTATGGGGCCAGCAGGCTTCTGGATAGGCTTTATTATTGGTCTGACGTCGGCAGCCATTATGATGATGTTGCGTATGCGGTTCCTGCAACGTCTGCCGTCAGCCATCATTCTGCAACGAGCATCCCg                                                   <  1:785215/139‑1 (MQ=255)

                                                                                          gAACCTATGGGGCCAGCAGGCTTCTGGATAGGCTTTATTATTGGTCTGACGTCGGCAGCCATTATGATGATGTTGCGTATGc                                                                                                    >  1:683881/1‑82 (MQ=255)

                                                                                          gAACCTATGGGGCCAGCAGGCTTCTGGATAGGCTTTATTATTGGTCTGACGTCGGCAGCCATTATGATGATGTTGCGTATGc                                                                                                    <  2:683881/82‑1 (MQ=255)

                                                                                                     gCCAGCAGGCTTCTGGATAGGCTTTATTATTGGTCTGACGTCGGCAGCCATTATGATGATGTTGCGTATGCGGTTCCTGCAACGTCTGCCGTCAGCCATCATTCTGCAACGAGCATCCCGCTAATAAAGACAAGGCGCa                                <  2:1117605/139‑1 (MQ=255)

                                                                                                        agcagGCTTCTGGATAGGCTTTATTATTGGTCTGACGTCGGc                                                                                                                              <  2:1412977/42‑1 (MQ=255)

                                                                                                        agcagGCTTCTGGATAGGCTTTATTATTGGTCTGACGTCGGc                                                                                                                              >  1:1412977/1‑42 (MQ=255)

                                                                                                                  tGGATAGGCTTTATTATTGGTCTGACGTCGGCAGCCATTATGATGATGTTGCGTATGCGGTTCCTGCAACGTCTGCCGTCAGCCATCATTCTGCAACGAGCATCCCGCTAATAAAGACAAGGCGCAACCTTCACGGGtt                   >  1:1109922/1‑139 (MQ=255)

                                                                                                                    gATAGGCTTTATTATTGGTCTGACGTCGGCAGCCATTATGATGATGTTGCGTATGCGGTTCCTGCAACGTCTGCCGTCAGCCATCATTCTGCAACGAGCATCCCGCTAATAAAGACAAGGCGCAACCTTCACGGGTTgc                 >  2:998240/1‑139 (MQ=255)

                                                                                                                         gCTTTATTATTGGTCTGACGTCGGCAGCCATTATGATGATGTTGCGTATGCGGTTCCTGCAACGTCTGCCGTCAGCca                                                                         >  2:289011/1‑78 (MQ=255)

                                                                                                                         gCTTTATTATTGGTCTGACGTCGGCAGCCATTATGATGATGTTGCGTATGCGGTTCCTGCAACGTCTGCCGTCAGCca                                                                         <  1:289011/78‑1 (MQ=255)

                                                                                                                         gCTTTATTATTGGTCTGACGTCGGCAGCCATTATGATGATGTTGCGTATGCGGTTCCTGCAACGTCTGCCGTCAGCCATCATTCTGCAACGAGCATcc                                                     <  2:1023085/98‑1 (MQ=255)

                                                                                                                         gCTTTATTATTGGTCTGACGTCGGCAGCCATTATGATGATGTTGCGTATGCGGTTCCTGCAACGTCTGCCGTCAGCCATCATTCTGCAACGAGCATcc                                                     >  1:1023085/1‑98 (MQ=255)

                                                                                                                              attattGGTCTGACGTCGGCAGCCATTATGATGATGTTGCGTATGCGGTTCCTGCAACGTCTGCCGTCAGc                                                                           <  2:646223/71‑1 (MQ=255)

                                                                                                                              attattGGTCTGACGTCGGCAGCCATTATGATGATGTTGCGTATGCGGTTCCTGCAACGTCTGCCGTCAGc                                                                           >  1:646223/1‑71 (MQ=255)

                                                                                                                                   tGGTCTGACGTCGGCAGCCATTATGATGATGTTGCGTAt                                                                                                      <  2:154513/39‑1 (MQ=255)

                                                                                                                                   tGGTCTGACGTCGGCAGCCATTATGATGATGTTGCGTATGCGGTTCCTGCAACGTCTGCCGTCAGCCATCATTCTGCAACGAGCATCCCGCTAATAAAGACAAGGCGCAACCTTCACGGGTTGCGCCTGTATTTTTACg  >  2:247045/1‑139 (MQ=255)

ACGCGTTCCATTTTCTATATTACCTTTACGGCTTACTGGGTGCTGGGCTTGCCAAGCGGCTATATTCTGGCACTGACCGATCTGGTCGTTGAACCTATGGGGCCAGCAGGCTTCTGGATAGGCTTTATTATTGGCCTGACGTCGGCAGCCATTATGATGATGTTGCGTATGCGGTTCCTGCAACGTCTGCCGTCAGCCATCATTCTGCAACGAGCATCCCGCTAATAAAGACAAGGCGCAACCTTCACGGGTTGCGCCTGTATTTTTACG  >  NC_000913/1744606‑1744875

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `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