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
A6 F1 I2 R1	758	59.3	2864096	93.9%	2689386	105.7

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%	103.2 / NA	33	G428G (GGC→GGT)	mdtK	multidrug efflux system transporter
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (18/15); total (18/15)

ACGCGTTCCATTTTCTATATTACCTTTACGGCTTACTGGGTGCTGGGCTTGCCAAGCGGCTATATTCTGGCACTGACCGATCTGGTCGTTGAACCTATGGGGCCAGCAGGCTTCTGGATAGGCTTTATTATTGGCCTGACGTCGGCAGCCATTATGATGATGTTGCGTATGCGGTTCCTGCAACGTCTGCCGTCAGCCATCATTCTGCAACGAGCATCCCGCTAATAAAGACAAGGCGCAACCTTCACGGGTTGCGCCTGTATTTTTACG  >  NC_000913/1744606‑1744875

aCGCGTTCCATTTTCTATATTACCTTTACGGCTTACTGGGTGCTGGGCTTGCCAAGCGGCTATATTCTGGCACTGACCGATCTGGTCGTTGAACCTATGGGGCCAGCAGGCTTCTGGATAGGCTTTATTATTGGTCTGa                                                                                                                                     >  1:873335/1‑139 (MQ=255)

aCGCGTTCCATTTTCTATATTACCTTTACGGCTTACTGGGTGCTGGGCTTGCCAAGCGGCTATATTCTGGCACTGACCGATCTGGTCGTTGAACCTATGGGGCCAGCAGGCTTCTGGATAGGCTTTATTATTGGTCTGa                                                                                                                                     >  1:445956/1‑139 (MQ=255)

                  atTACCTTTACGGCTTCCTGGGTGCTGGGCTTGCCAAGCGGCTATATTCTGGCACTGACCGATCTGGTCGTTGAACCTATGGGGCCAGCAGGCTTCTGGATAGGCTTTATTATTGGTCTGACGTCGGCAGCCATTatga                                                                                                                   <  2:253178/139‑1 (MQ=255)

                  atTACCTTTACGGCTTACTGGGTGCTGGGCTTGCCAAGCGGCTATATTCTGGCACTGACAGATCTGGTCGTTGAACCTATGGGGCCAGCAGGCTTCTGGATAGGCTTTATTATTGGTCTGACGTCGGCAGCCATTatga                                                                                                                   <  2:873335/139‑1 (MQ=255)

                         ttACGGCTTACTGGGTGCTGGGCTTGCCAAGCGGCTATATTCTGGCACTGACCGATCTGGTCGTTGAACCTATGGGGCCAGCAGGCTTCTGGATAGGCTTTATTATTGGTCTGACGTCGGCAGCCATTATGATGATGtt                                                                                                            >  1:159774/1‑139 (MQ=255)

                           aCGGCTTACTGGGTGCTGGGCTTGCCAAGCGGCTATATTCTGGCACTGACCGATCTGGTCGTTGAACCTATGGGGCCAGCAGGCTTCTGGATAGGCTTTATTATTGGTCTGACGTCGGCAGCCATTATGATGATGTTGc                                                                                                          >  1:410127/1‑139 (MQ=255)

                                  aCTGGGTGCTGGGCTTGCCAAGCGGCTATATTCTGGCACTGACCGATCTGGTCGTTGAACCTATGGGGCCAGCAGGCTTCTGGATAGGCTTTATTATTGGTCTGACGTCGGCAGCCATTATGATGATGTTGCGTATGCg                                                                                                   >  1:312855/1‑139 (MQ=255)

                                                  gCCAAGCGGCTATATTCTGGCACTGACCGATCTGGTCGTTGAACCTATGGGGCCAGCAGGCTTCTGGATAGGCTTTATTATTGGTCTGACGTCGGc                                                                                                                              >  1:311964/1‑96 (MQ=255)

                                                  gCCAAGCGGCTATATTCTGGCACTGACCGATCTGGTCGTTGAACCTATGGGGCCAGCAGGCTTCTGGATAGGCTTTATTATTGGTCTGACGTCGGc                                                                                                                              <  2:311964/96‑1 (MQ=255)

                                                  gCCAAGCGGCTATATTCTGGCACTGACCGATCTGGTCGTTGAACCTATGGGGCCAGCAGGCTTCTGGATAGGCTTTATTATTGGTCTGACGTCGGCAGCCATTATGATGATGTTGCGTATGCGGTTCCTGCAACGTCTg                                                                                   >  2:507342/1‑139 (MQ=255)

                                                  gCCAAGCGGCTATATTCTGGCACTGACCGATCTGGTCGTTGAACCTATGGGGCCAGCAGGCTTCTGGATAGGCTTTATTATTGGTCTGACGTCGGCAGCCATTATGATGATGTTGCGTATGCGGTTCCTGCAACGTCTg                                                                                   >  1:291780/1‑139 (MQ=255)

                                                                        cTGACCGATCTGGTCGTTGAACCTATGGGGCCAGCAGGCTTCTGGATAGGCTTTATTATTGGTCTGACGTCGGCAGCCATTATGATGATGTTGCGTATGCGGTTCCTGCAACGTCTGCCGTCAGCCATCATTCTGCAAc                                                             >  1:1161184/1‑139 (MQ=255)

                                                                           aCCGATCTGGTCGTTGAACCTATGGGGCCAGCAGGCTTCTGGATAGGCTTTATTATTGGTCTGACGTCGGc                                                                                                                              <  2:782546/71‑1 (MQ=255)

                                                                           aCCGATCTGGTCGTTGAACCTATGGGGCCAGCAGGCTTCTGGATAGGCTTTATTATTGGTCTGACGTCGGc                                                                                                                              >  1:782546/1‑71 (MQ=255)

                                                                           aCCGATCTGGTCGTTGAACCTATGGGGCCAGCAGGCTTCTGGATAGGCTTTATTATTGGTCTGACGTCGGCAGCCATTatgatg                                                                                                                 >  1:1241517/1‑84 (MQ=255)

                                                                           aCCGATCTGGTCGTTGAACCTATGGGGCCAGCAGGCTTCTGGATAGGCTTTATTATTGGTCTGACGTCGGCAGCCATTatgatg                                                                                                                 <  2:1241517/84‑1 (MQ=255)

                                                                           aCCGATCTGGTCGTTGAACCTATGGGGCCAGCAGGCTTCTGGATAGGCTTTATTATTGGTCTGACGTCGGCAGCCATTATGATGATGTTGCGTATGc                                                                                                    >  1:1216566/1‑97 (MQ=255)

                                                                           aCCGATCTGGTCGTTGAACCTATGGGGCCAGCAGGCTTCTGGATAGGCTTTATTATTGGTCTGACGTCGGCAGCCATTATGATGATGTTGCGTATGc                                                                                                    >  1:1066146/1‑97 (MQ=255)

                                                                           aCCGATCTGGTCGTTGAACCTATGGGGCCAGCAGGCTTCTGGATAGGCTTTATTATTGGTCTGACGTCGGCAGCCATTATGATGATGTTGCGTATGc                                                                                                    <  2:1216566/97‑1 (MQ=255)

                                                                           aCCGATCTGGTCGTTGAACCTATGGGGCCAGCAGGCTTCTGGATAGGCTTTATTATTGGTCTGACGTCGGCAGCCATTATGATGATGTTGCGTATGc                                                                                                    <  2:1066146/97‑1 (MQ=255)

                                                                             cGATCTGGTCGTTGAACCTATGGGGCCAGCAGGCTTCTGGATAGGCTTTATTATTGGTCTGACGTCGGCAGCCATTATGATGATGTTGCGTATGCGGTTCCTGCAACGTCTGCCGTCAGCCATCATTCTGCAACGAGCa                                                        <  2:604222/139‑1 (MQ=255)

                                                                                  tGGTCGTTGAACCTATGGGGCCAGCAGGCTTCTGGATAGGCTTTATTATTGGTCTGACGTCGGCAGCCATTATGATGATGTTGCGTATGCGGTTCCTGCAACGTCTGCCGTCAGCCATCATTCTGCAACGAGCATCCCg                                                   <  2:1161184/139‑1 (MQ=255)

                                                                                          gAACCTATGGGGCCAGCAGGCTTCTGGATAGGCTTTATTATTGGTCTGACGTCGGCAGCCATTATGATGATGTTGCGTATGCGGTTCCTGCAACGTCTGCCg                                                                                <  2:223461/102‑1 (MQ=255)

                                                                                          gAACCTATGGGGCCAGCAGGCTTCTGGATAGGCTTTATTATTGGTCTGACGTCGGCAGCCATTATGATGATGTTGCGTATGCGGTTCCTGCAACGTCTGCCg                                                                                >  1:223461/1‑102 (MQ=255)

                                                                                             ccTATGGGGCCAGCAGGCTTCTGGATAGGCTTTATTATTGGTCTGACGTCGGCAGCCATTATGATGATGTTGCGTATGCGGTTCCTGCAACGTCTGCCGTCAGCCATCATTCTGCAACGAGCATCCCGCTAATAAAGAc                                        <  2:291780/139‑1 (MQ=255)

                                                                                             ccTATGGGGCCAGCAGGCTTCTGGATAGGCTTTATTATTGGTCTGACGTCGGCAGCCATTATGATGATGTTGCGTATGCGGTTCCTGCAACGTCTGCCGTCAGCCATCATTCTGCAACGAGCATCCCGCTAATAAAGAc                                        <  2:410127/139‑1 (MQ=255)

                                                                                                      ccAGCAGGCTTCTGGATAGGCTTTATTATTGGTCTGACGTCGGCAGCCATTATGATGATGTTGCGTATGCGGTTCCTGCAACGTCTGCCGTCAGCCATCATTCTGCAACGAGCATCCCGCTAATAAAGACAAGGCGCaa                               >  1:266478/1‑139 (MQ=255)

                                                                                                        agcagGCTTCTGGATAGGCTTTATTATTGGTCTGACGTCGGCAGCCATTATGATGATGTTGCGTATGCGGTTCCTGCAACGTCTGCCGTCAGCCATCATTCTGCAACGAGCATCCCg                                                   <  2:1169906/117‑1 (MQ=255)

                                                                                                        agcagGCTTCTGGATAGGCTTTATTATTGGTCTGACGTCGGCAGCCATTATGATGATGTTGCGTATGCGGTTCCTGCAACGTCTGCCGTCAGCCATCATTCTGCAACGAGCATCCCg                                                   >  1:1169906/1‑117 (MQ=255)

                                                                                                                       aGGCTTTATTATTGGTCTGACGTCGGCAGCCATTATGATTATGTTGCGTATGCGGTTCCTGCAACGTCTGcc                                                                                 <  2:849261/72‑1 (MQ=255)

                                                                                                                       aGGCTTTATTATTGGTCTGACGTCGGCAGCCATTATGATGATGTTGCGTATGCGGTTCCTGCAACGTCTGcc                                                                                 >  1:849261/1‑72 (MQ=255)

                                                                                                                           tttATTATTGGTCTGACGTCGGCAGCCATTATGATGATGTTGCGTATGCGGTTCCTGCAACGTCTGCCGTCAGCCATCATTCTGCAACGAGCATCCCGCTAATAAAGACAAGGCGCAACCTTCACGGGTTGCGCCTGTa          >  1:1061133/1‑139 (MQ=255)

                                                                                                                                   tGGTCTGACGTCGGCAGCCATTATGATGATGTTGCGTATGCGGTTCCTGCAACGTCTGCCGTCAGCCATCATTCTGCAACGAGCATCCCGCTAATAAAGACAAGGCGCAACCTTCACGGGTTGCGCCTGTATTTTTACg  <  2:1137572/139‑1 (MQ=255)

ACGCGTTCCATTTTCTATATTACCTTTACGGCTTACTGGGTGCTGGGCTTGCCAAGCGGCTATATTCTGGCACTGACCGATCTGGTCGTTGAACCTATGGGGCCAGCAGGCTTCTGGATAGGCTTTATTATTGGCCTGACGTCGGCAGCCATTATGATGATGTTGCGTATGCGGTTCCTGCAACGTCTGCCGTCAGCCATCATTCTGCAACGAGCATCCCGCTAATAAAGACAAGGCGCAACCTTCACGGGTTGCGCCTGTATTTTTACG  >  NC_000913/1744606‑1744875

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A