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
A5 F17 I0 R1	87	56.5	4283937	98.6%	4223961	62.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	1,303,631	C→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	1,303,631	0	C	T	100.0%	169.7 / NA	58	Q246Y (CAG→TAT)	oppA	oligopeptide transporter subunit
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (31/27); total (31/27)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

AAACGAACGAATCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACCAGGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGTAGTGGTG  >  W3110S.gb/1303567‑1303691

aaaCGAACGAATCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTaa                                                        >  1:479269/1‑71 (MQ=255)

 aacgaacgAATCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAAc                                                       >  1:2251040/1‑71 (MQ=255)

 aacgaacgAATCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAAc                                                       >  1:161524/1‑71 (MQ=255)

  acgaacgaATCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAAcc                                                      <  1:2786845/71‑1 (MQ=255)

    gaacgaaTCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTa                                                    <  1:1874998/71‑1 (MQ=255)

        gaaTCGTTCTTGAACGCAGCCCGACCTACTGGACCAACGCGAAAACCGTTATTAACTATGTAACCTAtt                                                  >  1:4232478/1‑69 (MQ=255)

          aTCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGcc                                              <  1:869725/71‑1 (MQ=255)

          aTCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGcc                                              <  1:3883920/71‑1 (MQ=255)

           tCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGcc                                              >  1:673480/1‑70 (MQ=255)

           tCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCt                                             <  1:2136116/71‑1 (MQ=255)

             gTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTAt                                           <  1:2799442/71‑1 (MQ=255)

             gTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTAt                                           <  1:2794322/71‑1 (MQ=255)

               tCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTAtt                                                  >  1:4124236/1‑62 (MQ=255)

                    aaCGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCt                                    <  1:3059668/71‑1 (MQ=255)

                     aCGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAAcc                                                      <  1:1825477/52‑1 (MQ=255)

                     aCGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTg                                   <  1:2311218/71‑1 (MQ=255)

                     aCGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATAAACTATGTAACCTATTTGCCTATTGCTTCTg                                   <  1:484835/71‑1 (MQ=255)

                        cAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAg                                >  1:1578604/1‑71 (MQ=255)

                            ccGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCtt                                      <  1:3398033/61‑1 (MQ=255)

                            ccGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTa                             <  1:866872/70‑1 (MQ=255)

                             cGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTa                                                    <  1:3031910/46‑1 (MQ=39)

                             cGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTAcc                           <  1:2200592/71‑1 (MQ=255)

                              gACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCg                          <  1:1281141/71‑1 (MQ=255)

                                ccTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGAt                        <  1:1951610/71‑1 (MQ=255)

                                  tACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTa                                            <  1:2778380/49‑1 (MQ=39)

                                   aCTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGt                      >  1:1430164/1‑70 (MQ=255)

                                    cTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTAt                                                   >  1:2447473/1‑40 (MQ=38)

                                    cTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTc                     <  1:2261622/70‑1 (MQ=255)

                                    cTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCa                    <  1:3194763/71‑1 (MQ=255)

                                     tGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGAt                        >  1:3839177/1‑66 (MQ=255)

                                     tGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGAt                        >  1:1540168/1‑66 (MQ=255)

                                      ggAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAAc                  >  1:2665764/1‑71 (MQ=255)

                                       gAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTAt                                           >  1:3312051/1‑45 (MQ=38)

                                       gAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTAc                            >  1:2354909/1‑60 (MQ=255)

                                       gAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAAcc                 >  1:258255/1‑71 (MQ=255)

                                       gAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAAcc                 >  1:3841093/1‑71 (MQ=255)

                                        aacaacGCGAAAACCGTTATTAACTATGTAACCTAtt                                                  >  1:14069/1‑37 (MQ=37)

                                        aacaacGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCg                >  1:3193697/1‑71 (MQ=255)

                                         acaacGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCg                >  1:3535201/1‑70 (MQ=255)

                                         acaacGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGc               <  1:1298245/71‑1 (MQ=255)

                                          caacGCGAAAACCGTTATTAACTATGTAACCTATTTGcc                                              <  1:2965094/39‑1 (MQ=37)

                                            acGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCg                          >  1:3252471/1‑57 (MQ=255)

                                            acGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCg                          >  1:464944/1‑57 (MQ=255)

                                            acGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTAc            <  1:541679/71‑1 (MQ=255)

                                              gcgAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCaa                   >  1:2481807/1‑62 (MQ=255)

                                              gcgAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCaa                   >  1:2490885/1‑62 (MQ=255)

                                               cgAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGaa                                 <  1:1121063/47‑1 (MQ=39)

                                               cgAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCg          >  1:924915/1‑70 (MQ=255)

                                               cgAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCg          >  1:3746068/1‑70 (MQ=255)

                                                 ataaCCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTc                     <  1:3095529/55‑1 (MQ=255)

                                                 aaaaCCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGa                         <  1:2741502/53‑1 (MQ=255)

                                                  aaaCCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAg                                >  1:2166500/1‑45 (MQ=38)

                                                   aaCCGTTATTAACTATGTAACCTATTTGCCTATTGCTTc                                     >  1:1648414/1‑39 (MQ=37)

                                                   aaCCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGTAgtg     >  1:3338298/1‑71 (MQ=255)

                                                      cGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGTAgtggtg  <  1:1954003/71‑1 (MQ=255)

                                                        ttattaACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTa                             >  1:2432013/1‑42 (MQ=38)

                                                          attaACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGc               >  1:1960162/1‑54 (MQ=255)

                                                           ttaACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCg                          >  1:476754/1‑42 (MQ=38)

AAACGAACGAATCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACCAGGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGTAGTGGTG  >  W3110S.gb/1303567‑1303691

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A