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 F17 I0 R2	276	45.3	3729697	93.0%	3468618	60.6

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%	174.6 / NA	59	Q246Y (CAG→TAT)	oppA	oligopeptide transporter subunit
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (35/24); total (35/24)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

AACGAACGAATCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACCAGGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGTAGTGGTGAA  >  W3110S.gb/1303568‑1303693

aacgaacgAATCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTa                                                           >  1:1196517/1‑69 (MQ=255)

aacgaacgAATCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTa                                                           >  1:2449876/1‑69 (MQ=255)

aacgaacgAATCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTa                                                           >  1:1354449/1‑69 (MQ=255)

aacgaacgAATCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTa                                                           >  1:3042712/1‑69 (MQ=255)

aacgaacgAATCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTa                                                           >  1:595830/1‑69 (MQ=255)

aacgaacgAATCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTa                                                           >  1:327803/1‑69 (MQ=255)

aacgaacgAATCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTa                                                           >  1:3331770/1‑69 (MQ=255)

     acgaaTCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTa                                                      >  1:746857/1‑69 (MQ=255)

        aaTCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTAttt                                                   <  1:2141037/69‑1 (MQ=255)

         aTCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTg                                                  <  1:1882096/69‑1 (MQ=255)

         aTCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTg                                                  <  1:559995/69‑1 (MQ=255)

           cGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGcc                                                <  1:2240922/69‑1 (MQ=255)

               cTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAAcc                                                        >  1:2495131/1‑57 (MQ=255)

               cTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTAtt                                            >  1:167466/1‑69 (MQ=255)

                  gAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTa                                                      >  1:1995594/1‑56 (MQ=255)

                           ccGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTg                                     >  1:898815/1‑64 (MQ=255)

                           ccGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGtt                                <  1:433247/69‑1 (MQ=255)

                              aCCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTAcc                             <  1:1968295/69‑1 (MQ=255)

                              aCCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTAcc                             <  1:2843892/69‑1 (MQ=255)

                               ccTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTAcc                             <  1:139515/68‑1 (MQ=255)

                                cTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTAcc                             >  1:1940487/1‑67 (MQ=255)

                                cTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCg                            >  1:1870627/1‑68 (MQ=255)

                                cTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCg                            >  1:710897/1‑68 (MQ=255)

                                cTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCg                            >  1:14241/1‑68 (MQ=255)

                                cTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCg                            >  1:2239293/1‑68 (MQ=255)

                                cTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCg                            >  1:2243665/1‑68 (MQ=255)

                                cTACTGGAACAACGCGAAAACCGTTATTAACTA‑‑TAACCTATTTGcc                                                <  1:1656240/46‑1 (MQ=37)

                                  aCTGGAACAACGCGAAAACCGTTATTAACTATGTAACCt                                                       >  1:1300379/1‑39 (MQ=37)

                                  aCTGGAACAACGCGAAAACCGTTATTAACTATGTAACCt                                                       >  1:245063/1‑39 (MQ=37)

                                  aCTGGAACAACGCGAAAACCGTTATTAACTATGTAACCt                                                       >  1:1536776/1‑39 (MQ=37)

                                  aCTGGAACAACGCGAAAACCGTTATTAACTATGTAACCt                                                       >  1:1781105/1‑39 (MQ=37)

                                   cTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATg                         >  1:2594245/1‑68 (MQ=255)

                                   cTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATg                         >  1:2598637/1‑68 (MQ=255)

                                     ggAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCa                      <  1:286119/69‑1 (MQ=255)

                                     ggAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCa                      <  1:1593177/69‑1 (MQ=255)

                                     ggAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCa                      <  1:405724/69‑1 (MQ=255)

                                      gAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTg                                           >  1:1542644/1‑47 (MQ=39)

                                      gAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGc                                          >  1:743774/1‑48 (MQ=39)

                                      gAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGc                                          >  1:177528/1‑48 (MQ=39)

                                      gAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCaa                     >  1:2712528/1‑69 (MQ=255)

                                      gAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCa                      >  1:2491502/1‑68 (MQ=255)

                                          aacGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGc                 >  1:3462682/1‑69 (MQ=255)

                                          aacGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGc                 >  1:420343/1‑69 (MQ=255)

                                          aacGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGc                 >  1:3527250/1‑69 (MQ=255)

                                          aacGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGc                 >  1:2133879/1‑69 (MQ=255)

                                           acGCGAAAACCGTTATTAACTATGTAACCTATTTGcc                                                <  1:3420750/37‑1 (MQ=37)

                                           acGCGAAAACCGTTATTAACTATGTAACCTATTTGcc                                                <  1:3668289/37‑1 (MQ=37)

                                           acGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCt                >  1:206713/1‑69 (MQ=255)

                                            cgcgAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTa               >  1:68977/1‑69 (MQ=255)

                                                aaaaCCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGt           <  1:3702497/69‑1 (MQ=255)

                                                aaaaCCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGt           <  1:3048091/69‑1 (MQ=255)

                                                aaaaCCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGt           <  1:2597467/69‑1 (MQ=255)

                                                aaaaCCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGt           <  1:1326176/69‑1 (MQ=255)

                                                aaaaCCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGt           <  1:945170/69‑1 (MQ=255)

                                                 aaaCCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGt           <  1:234222/68‑1 (MQ=255)

                                                    ccGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTAcc                             <  1:1803953/47‑1 (MQ=39)

                                                    ccGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTAcc                             <  1:2936364/47‑1 (MQ=39)

                                                    ccGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTAcc                             <  1:2504983/47‑1 (MQ=39)

                                                         attaACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGTAGTGGTGaa  <  1:907837/69‑1 (MQ=255)

AACGAACGAATCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACCAGGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGTAGTGGTGAA  >  W3110S.gb/1303568‑1303693

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