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 F3 I0 R1	560	56.4	4650532	94.9%	4413354	59.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	1,303,633	G→T	100%	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	1,303,633	0	G	T	100.0%	172.8 / NA	58	Q246Y (CAG→TAT)	oppA	oligopeptide transporter subunit
Reads supporting (aligned to +/- strand): ref base G (0/0); new base T (29/29); total (29/29)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CGAACGAATCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACCAGGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGTAGTGGTGA  >  W3110S.gb/1303570‑1303692

cgaacgaaTCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCt                                                      <  1:2404984/71‑1 (MQ=255)

cgaacgaaTCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCt                                                      <  1:4263134/71‑1 (MQ=255)

cgaacgaaTCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCt                                                      <  1:4187154/71‑1 (MQ=255)

 gaacgaaTCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTa                                                     <  1:1472899/71‑1 (MQ=255)

  aacgaaTCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTAt                                                    <  1:2893083/71‑1 (MQ=255)

  aacgaaTCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTAt                                                    >  1:3733261/1‑71 (MQ=255)

         cGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGc                                                >  1:2636362/1‑68 (MQ=255)

          gTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTa                                             <  1:3995821/70‑1 (MQ=255)

           ttCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTAtt                                           >  1:88677/1‑71 (MQ=255)

               tGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCtt                                       >  1:2523943/1‑71 (MQ=255)

                gAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCt                                        <  1:2857269/69‑1 (MQ=255)

                 aaCGCAGCCCGACCTACTGGATCAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTc                                      <  1:4206876/70‑1 (MQ=255)

                  aCGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTg                                    <  1:776315/71‑1 (MQ=255)

                    gCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGaa                                  <  1:1759119/71‑1 (MQ=255)

                       gCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGtt                               <  1:725050/71‑1 (MQ=255)

                          cGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTAcc                            <  1:3813091/71‑1 (MQ=255)

                          cGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTAcc                            <  1:4509445/71‑1 (MQ=255)

                            aCCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCt                                                      <  1:3408690/43‑1 (MQ=38)

                              cTACTGGAACAACGCGAAAACCGTTATTAACTATGTa                                                          <  1:4375466/37‑1 (MQ=37)

                               tACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTa                                             <  1:441314/49‑1 (MQ=39)

                               tACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTAt                                            >  1:423874/1‑50 (MQ=255)

                               tACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTAt                                            >  1:3530242/1‑50 (MQ=255)

                                aCTGGAACAACGCGAAAACCGTTATTAACTATGTTACCTATTTGCCTATTGCTTCTGAAGTTACCGATGt                       >  1:1127982/1‑70 (MQ=255)

                                aCTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTAt                                                    >  1:2514493/1‑41 (MQ=38)

                                aCTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTAt                                                    >  1:4232752/1‑41 (MQ=38)

                                 cTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTAt                                            >  1:156449/1‑48 (MQ=39)

                                 cTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCtt                                       >  1:546526/1‑53 (MQ=255)

                                   ggAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCt                                              >  1:3412651/1‑44 (MQ=38)

                                   ggAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAAc                   >  1:237576/1‑71 (MQ=255)

                                    gAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGcc                                               >  1:3417561/1‑42 (MQ=38)

                                    gAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAAcc                  <  1:3421885/71‑1 (MQ=255)

                                    gAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAAcc                  >  1:548573/1‑71 (MQ=255)

                                    gAACAACGCGAAAAACGTTATTAACTATTTAACCTATTTGCCTATTGATTCTGAAg                                 >  1:3240209/1‑56 (MQ=255)

                                     aacaacGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTAcc                            <  1:1900143/60‑1 (MQ=255)

                                      acaacGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGaa                                  >  1:1910573/1‑53 (MQ=255)

                                      acaacGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGc                <  1:2749710/71‑1 (MQ=255)

                                       caacGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCt               <  1:3930594/71‑1 (MQ=255)

                                        aacGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGt                                >  1:2530001/1‑53 (MQ=255)

                                         acGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTAc             >  1:1390207/1‑71 (MQ=255)

                                           gcgAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCg           >  1:738872/1‑71 (MQ=255)

                                           gcgAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCg           <  1:1392573/71‑1 (MQ=255)

                                           gcgAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCg           <  1:44976/71‑1 (MQ=255)

                                            cgAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGt                                <  1:1859521/49‑1 (MQ=39)

                                             gAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGTa         <  1:543692/71‑1 (MQ=255)

                                              aaaaCCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAg                                 >  1:1300540/1‑46 (MQ=39)

                                               aaaCCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTg                                    >  1:1957955/1‑42 (MQ=38)

                                               aaaCCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTg                                    >  1:744263/1‑42 (MQ=38)

                                               aaaCCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGTAgt       >  1:765040/1‑71 (MQ=255)

                                                aaCCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTg                                    <  1:1790564/41‑1 (MQ=38)

                                                aaCCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGTAgtg      >  1:4021272/1‑71 (MQ=255)

                                                 aCCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGAt                         >  1:438298/1‑51 (MQ=255)

                                                   cGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGTAgtggt    >  1:615980/1‑70 (MQ=255)

                                                    gTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTAcc                            <  1:3843092/45‑1 (MQ=38)

                                                    gTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGTAGTGGTGa  <  1:2268251/71‑1 (MQ=255)

                                                    gTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGTAGTGGTGa  <  1:1385756/71‑1 (MQ=255)

                                                     ttattaACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGt          <  1:3927963/62‑1 (MQ=255)

                                                       attaACTATGTAACCTATTTGCCTATTGCTTCTGa                                   >  1:4490939/1‑35 (MQ=37)

                                                         taACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGTAgtggt    >  1:1915653/1‑64 (MQ=255)

CGAACGAATCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACCAGGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGTAGTGGTGA  >  W3110S.gb/1303570‑1303692

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