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
A9 F1 I2 R1	78	48.0	2243616	94.8%	2126947	114.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,253,271	G→A	A292V (GCC→GTC)	nupX ←	nucleoside permease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,253,271	0	G	A	100.0%	135.5 / NA	40	A292V (GCC→GTC)	nupX	nucleoside permease
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (21/19); total (21/19)

AGATAAGCGACAAATTCATTTATTGCCAGTTTCTGTCCAATCAAACTCCCGGCAAGATTCGCATCACTCCAGTCCACACCCATCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGGCATGTTCAAAACCAAACCAGCCACCAACGCCGCCGATAATACCGTTAATCAACGCAATTATTGCAACAAATGCCATCACCACTGTTGCCACACCTGCGGCGATTTTCAGCCCGGTCATTGCCCCTGTCGCA  >  NC_000913/2253139‑2253402

agaTAAGCGACAAATTCATTTATTGCCAGTTTCTGTCCAATCAAACTCCCGGCAAGATTCGCATCACTCCAGTCCACACCCATCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGtt                                                                                                                               <  1:997919/139‑1 (MQ=255)

  aTAAGCGACAAATTCATTTATTGCCAGTTTCTGTCCAATCAAACTCCCGGCAAGATTCGCATCACTCCAGTCCACACCCATCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCa                                                                                                                             >  1:1104531/1‑139 (MQ=255)

                       tGCCAGTTTCTGTCCAATCGAACTCCCGGCAAGATTCGCATCACTCCAGTCCACACCCATCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAAcg                                                                                                        >  2:1037867/1‑139 (MQ=255)

                           aGTTTCTGTCCAATCAAGCTCCCGGCAAGATTCGCATCACTCCAGTCCACACCCATCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAAcgccgc                                                                                                    <  2:912713/139‑1 (MQ=255)

                                 tGTCCAATCAAACTCCCGGCAAGATTCGCATCACTCCAGTCCACACCCATCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGataa                                                                                              <  1:694083/139‑1 (MQ=255)

                                   tCCAATCAAACTCCCGGCAAGATTCGCATCACTCCAGTCCACACCCATCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGataata                                                                                            >  1:435336/1‑139 (MQ=255)

                                        tCAAATTCCCGGCAAGATTCGCATCACTCCAGTCCACACCCATCACCCACGCCAGTGGAGACAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGATAATACCGtt                                                                                       >  1:461188/1‑139 (MQ=255)

                                        tCAAACTCCCGGCAAGATTCGCATCACTCCAGTCCACACCCATCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAAcg                                                                                                        <  1:1041055/122‑1 (MQ=255)

                                        tCAAACTCCCGGCAAGATTCGCATCACTCCAGTCCACACCCATCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAAcg                                                                                                        >  2:1041055/1‑122 (MQ=255)

                                             cTCCCGGCAAGATTCGCATCACTCCAGTCCACACCCATCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGATAATACCGTTAATCa                                                                                  >  1:1091935/1‑139 (MQ=255)

                                                  ggCAAGATTCGCATCACTCCAGTCCACACCCATCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGataa                                                                                              >  1:212156/1‑122 (MQ=255)

                                                  ggCAAGATTCGCATCACTCCAGTCCACACCCATCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGataa                                                                                              <  2:212156/122‑1 (MQ=255)

                                                  ggCAAGATTCGCATCACTCCAGTCCACACCCATCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGATAATACCGTTAATCAACGCa                                                                             >  2:677336/1‑139 (MQ=255)

                                                   gCAAGATTCGCATCACTCCAGTCCACACCCATCACCCACGCCAGTGGAGCCAGCAGGTACCCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGATAATACCGTTAATCAACGCaa                                                                            <  1:677336/139‑1 (MQ=255)

                                                      aGATTCGCATCACTCCAGTCCACACCCATCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGATAATACCGTTAATCAACGCAatta                                                                         >  2:575179/1‑139 (MQ=255)

                                                               tCACTCCAGTCCACACCCATCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGATAATACCGTTAATCAACGCAATTATTGcaacaa                                                                <  2:461188/139‑1 (MQ=255)

                                                                      aGTCCACACCCATCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGATAATACCGTTAATCAACGCAATTATTGCAACAAATGCCAt                                                         <  1:495935/139‑1 (MQ=255)

                                                                            cacCCATCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGATAATACCGTTAATCAACGCAATTATTGCAACAAATGCCATcaccac                                                   >  2:1092152/1‑139 (MQ=255)

                                                                             acCCATCACCCACGCCAGTGGAGTCAGCAGGTAACCTAAAATGGACTCCAGCTAGACATGTTCAAAACCAAACCAGCCACCAAcg                                                                                                        <  1:665219/85‑1 (MQ=255)

                                                                             acCCATCACCCACGCCAGTGGAGTCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTAAAAACCAAACCAGCCACCAAcg                                                                                                        >  2:665219/1‑85 (MQ=255)

                                                                             acCCATCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAAcgcc                                                                                                      >  2:506102/1‑87 (MQ=255)

                                                                             acCCATCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAAcgcc                                                                                                      <  1:506102/87‑1 (MQ=255)

                                                                             acCCATCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGataa                                                                                              <  1:255665/95‑1 (MQ=255)

                                                                             acCCATCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGATAATACCGTTAATCAACGCAATTATTGCAACAAATGCCATCACCACt                                                  <  2:1091935/139‑1 (MQ=255)

                                                                             acCCATCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGAACTCCAGCGAGACATGTTCAAAACCAAACCACCCACCAACGCCGCCGataa                                                                                              >  2:255665/1‑95 (MQ=255)

                                                                                 aTCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGATAATACCGTTAATCAACGCAATTATTGCAACAAATGCCATCACCACTGTTg                                              >  1:1070037/1‑139 (MQ=255)

                                                                                  tCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGATAATACCGTTAATCAACGCAATTATTGCAACaaa                                                               >  2:1021185/1‑121 (MQ=255)

                                                                                  tCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGATAATACCGTTAATCAACGCAATTATTGCAACaaa                                                               <  1:1021185/121‑1 (MQ=255)

                                                                                  tCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGATAATACCGTTAATCAACGCAATTATTGCAACAAATGCCATCACCACTGTTGc                                             >  1:509818/1‑139 (MQ=255)

                                                                                         cGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGa                                                                                                 >  2:135284/1‑80 (MQ=255)

                                                                                         cGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGa                                                                                                 <  1:135284/80‑1 (MQ=255)

                                                                                         cGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACAAGCCACCAACGCCGCCGATAATACCGTTAATCAACGCAATTATTGCAACAAATGCCATCACCACTGTTGCCACACCt                                      >  2:895018/1‑139 (MQ=255)

                                                                                                ggAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAAcgcc                                                                                                      >  2:100898/1‑68 (MQ=255)

                                                                                                ggAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAAcgcc                                                                                                      <  1:100898/68‑1 (MQ=255)

                                                                                                    ccAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAAcgccg                                                                                                     <  2:291035/65‑1 (MQ=255)

                                                                                                    ccAGCAGGTAACCTAAAATGGACTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAAcgccg                                                                                                     >  1:291035/1‑65 (MQ=255)

                                                                                                                         aCTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGATAATACCGTTAATCAACGCAATTATTGCAACAAAt                                                              >  2:327321/1‑83 (MQ=255)

                                                                                                                         aCTCCAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGATAATACCGTTAATCAACGCAATTATTGCAACAAAt                                                              <  1:327321/83‑1 (MQ=255)

                                                                                                                             cAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGATAATACCGTTAATCAACGCAATTATTGCAACAAATGCCATCACCACTGTTGCCACACCTGCGGCGATTTTCAGCCCGGTCATTGCCCCTGTCGCa  <  1:561640/139‑1 (MQ=255)

                                                                                                                             cAGCGAGACATGTTCAAAACCAAACCAGCCACCAACGCCGCCGATAATACCGTTAATCAACGCAATTATTGCAACAAATGCCATCACCACTGTTGCCACACCTGCGGCGATTTTCAGCCCGGTCATTGCCCCTGTCGCa  <  2:509818/139‑1 (MQ=255)

AGATAAGCGACAAATTCATTTATTGCCAGTTTCTGTCCAATCAAACTCCCGGCAAGATTCGCATCACTCCAGTCCACACCCATCACCCACGCCAGTGGAGCCAGCAGGTAACCTAAAATGGACTCCAGCGAGGCATGTTCAAAACCAAACCAGCCACCAACGCCGCCGATAATACCGTTAATCAACGCAATTATTGCAACAAATGCCATCACCACTGTTGCCACACCTGCGGCGATTTTCAGCCCGGTCATTGCCCCTGTCGCA  >  NC_000913/2253139‑2253402

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A