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 F1 I1 R1	770	51.4	2439994	93.8%	2288714	110.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,583,454	G→A	intergenic (+36/‑29)	yrhA → / → insA	pseudogene, interrupted by IS1E/IS1 repressor TnpA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,583,454	0	G	A	100.0%	98.6 / NA	33	intergenic (+36/‑29)	yrhA/insA	pseudogene, interrupted by IS1E/IS1 repressor TnpA
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (19/14); total (19/14)

TTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCGGACAT  >  NC_000913/3583334‑3583563

ttATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTg                                                                                             <  2:256579/139‑1 (MQ=255)

                 atTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCtt                                                                            <  2:599432/139‑1 (MQ=255)

                   ttCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCt                                                                          >  1:1055224/1‑139 (MQ=255)

                   ttCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCt                                                                          >  1:498435/1‑139 (MQ=255)

                               gATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATTACATTAAAGGTGATGCTGCCAAGTTACCGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTCGCTTCTGATTCTATCAGc                                                              >  1:589812/1‑139 (MQ=25)

                                aTCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCt                                                             >  2:495919/1‑139 (MQ=255)

                                      aaGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCcct                                                       >  2:341295/1‑139 (MQ=255)

                                          aCGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTg                                                   >  1:14095/1‑139 (MQ=255)

                                          aCGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGAATTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGc                                                              <  2:799823/128‑1 (MQ=255)

                                          aCGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGAATTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGc                                                              >  1:799823/1‑128 (MQ=255)

                                            ggTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGtt                                                 <  2:14095/139‑1 (MQ=255)

                                                      cGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGCGTTTTTGAGGTGCTCCAGTGGCtt                                                                            >  2:729916/1‑102 (MQ=255)

                                                      cGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGCGTTTTTGAGGTGCTCCAGTGGCtt                                                                            <  1:729916/102‑1 (MQ=255)

                                                        gggATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCtt                                                                            <  2:186092/100‑1 (MQ=255)

                                                        gggATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCtt                                                                            >  1:186092/1‑100 (MQ=255)

                                                        gggATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACg                                     >  1:400698/1‑139 (MQ=255)

                                                            ttATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGggt                                 >  1:544217/1‑139 (MQ=255)

                                                               taGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAgg                                                                                          >  1:657035/1‑79 (MQ=255)

                                                               taGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAgg                                                                                          <  2:657035/79‑1 (MQ=255)

                                                                    tttCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTa                         <  1:195694/139‑1 (MQ=255)

                                                                       cAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACg                      >  2:136441/1‑139 (MQ=255)

                                                                          tatTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAgg                                                                                          <  1:923522/68‑1 (MQ=255)

                                                                          tatTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAgg                                                                                          >  2:923522/1‑68 (MQ=255)

                                                                                 ttATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACgggg                                  >  2:474103/1‑117 (MQ=255)

                                                                                 ttATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACgggg                                  <  1:474103/117‑1 (MQ=255)

                                                                                      aCATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACggg                                   >  2:1167354/1‑111 (MQ=37)

                                                                                      aCATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACggg                                   <  1:1167354/111‑1 (MQ=37)

                                                                                      aCATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAg               <  2:356032/131‑1 (MQ=25)

                                                                                      aCATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAg               >  1:356032/1‑131 (MQ=25)

                                                                                          tAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTa                                           <  2:421627/99‑1 (MQ=18)

                                                                                          tAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTa                                           >  1:421627/1‑99 (MQ=18)

                                                                                          tAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGGACCGCCGGACa   >  2:794691/1‑139 (MQ=12)

                                                                                           aaaGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCGGACAt  <  1:485310/139‑1 (MQ=14)

TTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCGGACAT  >  NC_000913/3583334‑3583563

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A