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 F21 I0 R2	316	65.6	5147759	97.4%	5013917	60.3

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%	177.5 / NA	58	Q246Y (CAG→TAT)	oppA	oligopeptide transporter subunit
Reads supporting (aligned to +/- strand): ref base G (0/0); new base T (30/28); total (30/28)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

AACGAACGAATCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACCAGGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGTAGTGGTGAAATC  >  W3110S.gb/1303568‑1303696

aacgaacgAATCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAAc                                                            >  1:4192822/1‑71 (MQ=255)

    aacgaaTCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTAt                                                        >  1:2825351/1‑71 (MQ=255)

    aacgaaTCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTAt                                                        >  1:782894/1‑71 (MQ=255)

    aacgaaTCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTAt                                                        >  1:4345977/1‑71 (MQ=255)

    aacgaaTCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTAt                                                        >  1:4648411/1‑71 (MQ=255)

         aTCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGcc                                                   >  1:3264005/1‑71 (MQ=255)

          tCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGcc                                                   >  1:1434891/1‑70 (MQ=255)

          tCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCt                                                  <  1:1309208/71‑1 (MQ=255)

               cTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGc                                             >  1:2341539/1‑71 (MQ=255)

                  gAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTc                                          >  1:151870/1‑71 (MQ=255)

                   aaCGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCt                                         <  1:4545724/71‑1 (MQ=255)

                      gCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGaa                                      <  1:3690213/71‑1 (MQ=255)

                            cGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAg                                     >  1:4869737/1‑66 (MQ=255)

                            cGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGt                                    >  1:3292854/1‑67 (MQ=255)

                            cGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGt                                    >  1:503185/1‑67 (MQ=255)

                            cGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGt                                    >  1:3227885/1‑67 (MQ=255)

                            cGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTaat                                >  1:2528118/1‑69 (MQ=255)

                            cGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTaat                                >  1:27698/1‑69 (MQ=255)

                            cGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTAcc                                >  1:146134/1‑71 (MQ=255)

                            cGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTAcc                                <  1:2141507/71‑1 (MQ=255)

                              aCCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGa                              <  1:3372880/71‑1 (MQ=255)

                              aCCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGa                              <  1:197685/71‑1 (MQ=255)

                              aCCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGa                              <  1:675627/71‑1 (MQ=255)

                              aCCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGa                              <  1:1004002/71‑1 (MQ=255)

                                  aCTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTAtt                                                       >  1:2600570/1‑42 (MQ=38)

                                  aCTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTAtt                                                       >  1:4857161/1‑42 (MQ=38)

                                  aCTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGt                           >  1:4150156/1‑70 (MQ=255)

                                  aCTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGt                           >  1:5109148/1‑70 (MQ=255)

                                   cTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCt                                         >  1:891108/1‑55 (MQ=255)

                                   cTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTc                          <  1:1731686/70‑1 (MQ=255)

                                   cTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTc                          >  1:1785788/1‑70 (MQ=255)

                                   cTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCa                         <  1:4829274/71‑1 (MQ=255)

                                   cTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCa                         <  1:4677615/71‑1 (MQ=255)

                                    tGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGa                                       <  1:4627873/56‑1 (MQ=255)

                                    tGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGa                                       <  1:3992300/56‑1 (MQ=255)

                                    tGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCa                         <  1:716040/70‑1 (MQ=255)

                                     ggAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTgt                                       <  1:1089439/55‑2 (MQ=255)

                                      gAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGcc                                                   <  1:5140210/42‑1 (MQ=38)

                                      gAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGcc                                                   <  1:1462594/42‑1 (MQ=38)

                                      gAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTg                                              >  1:3970718/1‑47 (MQ=39)

                                      gAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCTATGTCAAc                       <  1:3701306/70‑1 (MQ=255)

                                      gAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGa                              >  1:1619677/1‑63 (MQ=255)

                                      gAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAAc                       <  1:1346233/70‑1 (MQ=255)

                                       aacaacGCGAAAACCGTTATTAACTATGTAACCTATTTGcc                                                   <  1:2953858/41‑1 (MQ=38)

                                        acaacGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTa                                                 >  1:3926222/1‑42 (MQ=38)

                                        acaacGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCaa                        >  1:5133444/1‑67 (MQ=255)

                                        acaacGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAAc                       <  1:3179503/68‑1 (MQ=255)

                                           acGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCtt                                           >  1:1336414/1‑45 (MQ=38)

                                           acGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAg                                     >  1:4869324/1‑51 (MQ=255)

                                           acGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGAt                             >  1:159532/1‑59 (MQ=255)

                                             gcgAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCg               <  1:2412114/71‑1 (MQ=255)

                                               gAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGt              <  1:4898783/70‑1 (MQ=255)

                                                aaaaCCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGTAGTTAcc                                <  1:2839672/51‑1 (MQ=255)

                                                     cGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGTa             >  1:4943877/1‑65 (MQ=255)

                                                      gTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGTAGTGGTGa      <  1:3206370/71‑1 (MQ=255)

                                                       ttattaACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTc                          <  1:7794/50‑1 (MQ=255)

                                                       ttattaACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTc                          <  1:1760/50‑1 (MQ=255)

                                                          ttaACTATGTAACCTTTTTGGCTATTGCTTCTGAAGTTAGCGATGTCAACCGCTACCGTAGTGGTGAAATc  <  1:3177954/71‑1 (MQ=255)

AACGAACGAATCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACCAGGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGTAGTGGTGAAATC  >  W3110S.gb/1303568‑1303696

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