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
A1 F28 I2 R2	356	55.1	4139924	95.4%	3949487	63.8

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	W3110S.gb	1,303,631	C→T	Q246Y (CAG→TAT)	oppA →	oligopeptide transporter subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	1,303,631	0	C	T	100.0%	175.5 / NA	56	Q246Y (CAG→TAT)	oppA	oligopeptide transporter subunit
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (28/28); total (28/28)

TAAACGAACGAATCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACCAGGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGTAGTGGTGAA  >  W3110S.gb/1303566‑1303693

tAAACGAACGAATCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTa                                                           <  1:1244104/71‑1 (MQ=255)

tAAACGAACGAATCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTa                                                           <  1:1276973/71‑1 (MQ=255)

tAAACGAACGAATCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTa                                                           <  1:2464374/71‑1 (MQ=255)

tAAACGAACGAATCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTa                                                           <  1:3418283/71‑1 (MQ=255)

           aTCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGcc                                                >  1:2728338/1‑71 (MQ=255)

           aTCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGcc                                                >  1:1105107/1‑71 (MQ=255)

           aTCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGcc                                                >  1:2784798/1‑71 (MQ=255)

           aTCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGcc                                                >  1:577863/1‑71 (MQ=255)

           aTCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGcc                                                >  1:2968814/1‑71 (MQ=255)

           aTCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGcc                                                >  1:1689367/1‑71 (MQ=255)

           aTCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGcc                                                >  1:3640987/1‑71 (MQ=255)

           aTCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGcc                                                >  1:3553406/1‑71 (MQ=255)

           aTCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGcc                                                >  1:3610720/1‑71 (MQ=255)

           aTCGTTCTTGAACGCAGACCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGcc                                                >  1:1374480/1‑71 (MQ=255)

              gTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTAt                                             <  1:3064984/71‑1 (MQ=255)

              gTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTAt                                             <  1:1953316/71‑1 (MQ=255)

              gTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTAt                                             <  1:3489666/71‑1 (MQ=255)

                    gAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGc                                          <  1:939168/68‑1 (MQ=255)

                    gAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCt                                         <  1:1458451/69‑1 (MQ=255)

                    gAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCt                                         <  1:3229138/69‑1 (MQ=255)

                    gAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCt                                         <  1:4000661/69‑1 (MQ=255)

                    gAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCt                                         <  1:1315078/69‑1 (MQ=255)

                               gACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCg                            <  1:1234461/71‑1 (MQ=255)

                                   tACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTa                               <  1:3631323/64‑1 (MQ=255)

                                   tACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTa                               <  1:1074637/64‑1 (MQ=255)

                                   tACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTa                               <  1:2725412/64‑1 (MQ=255)

                                      tGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCt                                         <  1:2719118/51‑1 (MQ=255)

                                       ggAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGa                                    <  1:21876/55‑1 (MQ=255)

                                       ggAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGa                                    <  1:3597075/55‑1 (MQ=255)

                                       ggAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGa                                    <  1:2003743/55‑1 (MQ=255)

                                       ggAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGa                                    <  1:3351855/55‑1 (MQ=255)

                                       ggAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGa                                    <  1:1354339/55‑1 (MQ=255)

                                       ggAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGa                                    <  1:2329012/55‑1 (MQ=255)

                                       ggAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCAGa                                    <  1:2603174/55‑1 (MQ=255)

                                         aacaacGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAg                                  >  1:773177/1‑55 (MQ=255)

                                         aacaacGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAg                                  >  1:484943/1‑55 (MQ=255)

                                         aacaacGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAg                                  >  1:2936230/1‑55 (MQ=255)

                                         aacaacGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAg                                  >  1:2854718/1‑55 (MQ=255)

                                         aacaacGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAg                                  >  1:3825064/1‑55 (MQ=255)

                                         aacaacGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAg                                  >  1:1414353/1‑55 (MQ=255)

                                         aacaacGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAg                                  >  1:1568457/1‑55 (MQ=255)

                                         aacaacGCGAAAACCGTTATTAACTATGTAACATATTTGc                                                 >  1:2779739/1‑40 (MQ=37)

                                          acaacGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAAc                    >  1:520575/1‑68 (MQ=255)

                                          acaacGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAAc                    >  1:1040141/1‑68 (MQ=255)

                                          acaacGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAAc                    >  1:3873775/1‑68 (MQ=255)

                                          acaacGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAAc                    >  1:1514605/1‑68 (MQ=255)

                                          acaacGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAAc                    >  1:198833/1‑68 (MQ=255)

                                          acaacGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAAc                    >  1:3333658/1‑68 (MQ=255)

                                          acaacGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAAc                    >  1:2983543/1‑68 (MQ=255)

                                                       cGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGTAgtggt     >  1:129663/1‑70 (MQ=255)

                                                       cGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGTAgtggt     >  1:250342/1‑70 (MQ=255)

                                                        gTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGTAgtggtg    >  1:3509412/1‑70 (MQ=255)

                                                         ttattaACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGTAGTGGTGaa  <  1:3528181/71‑1 (MQ=255)

                                                         ttattaACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGTAGTGGTGaa  <  1:1394703/71‑1 (MQ=255)

                                                         ttattaACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGTAGTGGTGaa  <  1:3285365/71‑1 (MQ=255)

                                                         ttattaACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGTAGTGGTGaa  <  1:23953/71‑1 (MQ=255)

TAAACGAACGAATCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACCAGGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGTAGTGGTGAA  >  W3110S.gb/1303566‑1303693

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 21 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A