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
A0 F0 I1 R1	715	38.4	1606192	96.6%	1551581	120.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,304,813	(C)_7→8	coding (1005/1245 nt)	mtr ←	tryptophan transporter of high affinity

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,304,806	1	.	C	100.0%	113.0 / NA	33	L338V (CTG→GTG)	mtr	tryptophan transporter of high affinity
Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (16/17); total (16/17)

CACCCCAGACGCGGAATTTCGGGCTGCCAAAGCGTTTACGCGATGCACGGGCTAACAGCGCCGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAG‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAGATAGTCAAACAAACCCAGCGTTACGCCGAGGAACGAA  >  NC_000913/3304668‑3304930

cACCCCAGACGCGGAATTTCGGGCTGCCAAAGCGTTTACGCGATGCACGGGCTAACAGCGCCGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAg                                                                                                                               >  2:575949/1‑139 (MQ=255)

                            aaaGCGTTTACGCGATGCACGGGCTAACAGCGCCGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGCCCCCCCCACAACTGGCGGGGCAAAGGt                                                                                                   <  2:433678/139‑1 (MQ=255)

                                               cGGGCTAACAGCGCCGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGCCCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCaat                                                                                <  2:491821/139‑2 (MQ=255)

                                                    tAACAGCGCCGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATATCCAATGGCGTACAGGAATCCGTTCGGGAACAACAGCCCCCCCCACAACAGGCGGGGCAAAGGTCAGCTATGCCGTTTTCAAGCGGcc                                                                           <  1:575949/139‑1 (MQ=255)

                                                     aaCAGCGCCGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGCCCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGccc                                                                          >  2:303178/1‑139 (MQ=255)

                                                     aaCAGCGCCGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGCCCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGccc                                                                          >  1:796705/1‑139 (MQ=255)

                                                     aaCAGCGCCGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAG‑ccc                                                                                                                           >  2:664596/1‑89 (MQ=255)

                                                     aaCAGCGCCGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAG‑ccc                                                                                                                           <  1:664596/89‑1 (MQ=255)

                                                            ccGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGCCCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCg                                                                   >  2:240009/1‑139 (MQ=255)

                                                                          gccCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGCCCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCa                                                     <  1:636645/139‑1 (MQ=255)

                                                                           cccAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGCCCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCaa                                                    <  2:611192/139‑1 (MQ=255)

                                                                            ccAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGCCCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCaaa                                                   <  2:1994/139‑1 (MQ=255)

                                                                                aTGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGCCCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGa                                               >  2:214090/1‑139 (MQ=255)

                                                                                  ggTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGCCCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATc                                             <  1:240420/139‑1 (MQ=255)

                                                                                        cggtAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGCCCCCCCCACAACTGGCGGGGCAAAGGTCAGGAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAg                                       <  1:529341/136‑1 (MQ=255)

                                                                                          cTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGCCCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGcc                                                                           <  2:149550/101‑1 (MQ=255)

                                                                                          cTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGCCCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGcc                                                                           >  1:149550/1‑101 (MQ=255)

                                                                                          cTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGCCCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAGAt                                     >  1:464417/1‑139 (MQ=255)

                                                                                          cTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGCCCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAGAt                                     >  2:290396/1‑139 (MQ=255)

                                                                                          cTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGCCCCCCCCACAACTGGCGGGGCAAAGGGCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAGAt                                     >  1:571505/1‑139 (MQ=255)

                                                                                           tAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGCCCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAGATa                                    <  2:796705/139‑1 (MQ=255)

                                                                                              aCCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGCCCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCaaa                                                   >  1:251551/1‑121 (MQ=255)

                                                                                              aCCAGCATAACCAATGGCGTACAGGAATCCGTTCGGAAACAACAGCCCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCaaa                                                   <  2:251551/121‑1 (MQ=255)

                                                                                                  gCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGCCCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGtcgtcg                                                           >  1:601879/1‑109 (MQ=255)

                                                                                                  gCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGCCCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGtcgtcg                                                           <  2:601879/109‑1 (MQ=255)

                                                                                                       aCCAATGGCGTACAGGAATCCGTTCGGGAACAACAGCCCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAGATAGTCAAACAAAcc                        <  1:240009/139‑1 (MQ=255)

                                                                                                             ggCGTACAGGAATCCGTTCGGGTACAACAGCCCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGCCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAGATAGTCAAACAAACCCAGCGt                  >  1:262029/1‑139 (MQ=255)

                                                                                                                 tACAGGAATCCGTTCGGGAACAACAGCCCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAGATAGTCAAACAAACCCAGCGTTACg              >  1:114134/1‑139 (MQ=255)

                                                                                                                        aTCCGTTCGGGAACAACAGCCCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAg                                       <  1:399235/107‑1 (MQ=255)

                                                                                                                        aTCCGTTCGGGAACAACAGCCCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAg                                       >  2:399235/1‑107 (MQ=255)

                                                                                                                        aTCCGTTCGGGAACAACAGCCCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAGa                                      <  2:126937/108‑1 (MQ=255)

                                                                                                                        aTCCGTTCGGGAACAACAGCCCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAGa                                      >  1:126937/1‑108 (MQ=255)

                                                                                                                        aTCCGTTCGGGAACAACAGCCCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAGATAGTCAAACAAACCCAGCGTTACGCCGAGga       >  1:218746/1‑139 (MQ=255)

                                                                                                                           cGTTCGGGAACAACAGCCCCCCCCACAACTGGCGGGGCa                                                                                                        <  1:721843/39‑1 (MQ=255)

                                                                                                                           cGTTCGGGAACAACAGCCCCCCCCACAACTGGCGGGGCa                                                                                                        >  2:721843/1‑39 (MQ=255)

                                                                                                                             ttCGGGAACAACAGCCCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAGATAGTCAAACAAACCCAGCGTTACGCCGAGgaacgaa  <  1:290396/139‑1 (MQ=255)

CACCCCAGACGCGGAATTTCGGGCTGCCAAAGCGTTTACGCGATGCACGGGCTAACAGCGCCGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAG‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAGATAGTCAAACAAACCCAGCGTTACGCCGAGGAACGAA  >  NC_000913/3304668‑3304930

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 15 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A