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
A13 F1 I1 R1	778	68.7	3228504	93.4%	3015422	109.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,556,033	A→G	Y273H (TAC→CAC)	rtcA ←	RNA 3'‑terminal phosphate cyclase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,556,033	0	A	G	100.0%	180.5 / NA	51	Y273H (TAC→CAC)	rtcA	RNA 3'‑terminal phosphate cyclase
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (23/28); total (23/28)

CTCCACCACCGCGATATTGGTCAGCAGATGGCATGAGGGATGGGCGACCGTAAATTCCCCCGCGCCCGCCAGCGCCATCGGTAGCACCAGTTGGTCAGCAAGATATT‑CCCCCACCGCCGCCGTGCTTGCCAGGTAGCGTTTCACCTCTTTCACCAACTGTGCCGCAACCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACC  >  NC_000913/3555899‑3556153

cTCCACCACCGCGATATTGGTCAGCAGATGGCATGAGGGATGGGCGACCGTAAATTCCCCCGCGCCCGCCAGCGCCATCGGTAGCACCAGTTGGTCAGCAAGATATT‑CCCCCACCGCCGCCGTGCTTGCCAGGTGGCGt                                                                                                                      >  1:1270248/1‑139 (MQ=255)

   caccacCGCGATATTGGTCAGCAGATGGCATGAGGGATGGGCGACCGTAAATTCCCCCGCGCCCGCCAGCGCCATCGGTAGCACCAGTTGGTCAGCAAGATATT‑CCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTc                                                                                                                   <  2:149322/139‑1 (MQ=255)

    accaccGCGATATTGGTCAGCAGATGGCATGAGGGTTGGGCGACCGTAAATTCCCCCGCGCCCGCCAGCGCCATCGGTAGCACCAGTTGGTCAGCAAGATATT‑CCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCa                                                                                                                  <  1:789451/139‑1 (MQ=255)

    accaccGCGATATTGGTCAGCAGATGGCATGAGGGATGGGCGACCGTAAATTCCCCCGCGCCCGCCAGCGCCATCGGTAGCACCAGTTGGTCAGCAAGATATT‑CCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCa                                                                                                                  <  2:1270248/139‑1 (MQ=255)

      caccGCGATATTGGTCAGCAGATGGCATGAGGGATGGGCGACCGTAAATTCCCCCGCGCCCGCCAGCGCCATCGGTAGCACCAGTTGGTCAGCAAGATATTCCCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCAc                                                                                                                 <  1:1535826/139‑1 (MQ=255)

       accGCGATATTGGTCAGCAGATGGCATGAGGGATGGGCGACCGTAAATTCCCCCGCGCCCGCCAGCGCCATCGGTAGCACCAGTTGGTCAACAAGATATT‑CCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACct                                                                                                               <  1:1440259/139‑1 (MQ=255)

       accACGATATTGGTCAGCAGATGGCATGAGGGATGGGCGACCGTAAATTCCCCCGCGCCCGCCAGCGCCATCGGTAGCACCAGTTGGTCAGCAAGATATT‑CCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACct                                                                                                               <  2:1046390/139‑1 (MQ=255)

          gcgATATTGGTCAGCAGATGGCATGAGGGATGGGCGACCGTAAATTCCCCCGCGCCCGCCAGCGCCATCGGTAGCACCAGTTGGTCAGCAAGATATT‑CCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACCTCtt                                                                                                            >  2:1498836/1‑139 (MQ=255)

                 tGGTCAGCAGATGGCATGAGGGATGGGCGACCGTAAATTCCCCCGCGCCCGCCAGCGCCATCGGTAGCACCAGTTGGTCAGCAAGATATT‑CCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACCTCTTTCACCaa                                                                                                     <  2:1570143/139‑1 (MQ=255)

                             ggCATGAGGGATGGGCGACCGTAAATTCCCCCGCGCCCGCCAGCGCCATCGGTAGCACCAGTTGGTCAGCAAGATATT‑CCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACCTCTTTCACCAACTGTGCCGCAac                                                                                         >  1:174861/1‑139 (MQ=255)

                                       aTGGGCGACCGTAAATTCCCCCGCGCCCGCCAGCGCCATCGGTAGCACCAGTTGGTCAGCAAGATATT‑CCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACCTCTTTCACCaa                                                                                                     <  2:1597452/117‑1 (MQ=255)

                                       aTGGGCGACCGTAAATTCCCCCGCGCCCGCCAGCGCCATCGGTAGCACCAGTTGGTCAGCAAGATATT‑CCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACCTCTTTCACCaa                                                                                                     >  1:1597452/1‑117 (MQ=255)

                                         gggCGACCGTAAATTCCCCCGCGCCCGCCAGCGCCATCGGTAGCACCAGTTGGTCAGCAAGATATT‑CCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCAGCTCTTTCACCAACTGTGCCGCAACCACCTCGGCACt                                                                             >  2:1011703/1‑139 (MQ=255)

                                         gggCGACCGTAAATTCCCCCGCGCCCGCCAGCGCCATCGGTAGCACCAGTTGGTCAGCAAGATATT‑CCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACCTCTTTCACCAACTGTGCCGCAACCACCTCGGCACt                                                                             >  2:1024169/1‑139 (MQ=255)

                                         gggCGACCGTAAATTCCCCCGCGCCCACCAGCGCCATCGGTAGCACCAGTTGGTCAGCAAGATATT‑CCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACCTCTTTCACCAACTGTGCCGCAACCACCTCGGCACt                                                                             >  1:1148267/1‑139 (MQ=255)

                                          ggCGACCGTAAATTCCCCCGCGCCCGCCAGCGCCATCGGTAGCACCAGTTGGTCAGCAAGATATT‑CCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACCTCTTTCACCAACTGTGCCGCAACCACCTCGGCACTg                                                                            <  2:1528148/139‑1 (MQ=255)

                                             gACCGTAAATTCCCCCGCGCCCGCCAGCGCCATCGGTAGCACCAGTTGGTCAGCAAGATATT‑CCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACCTCTTTCACCAACTGTGCCGCAACCACCTCGGCACTGAcg                                                                         <  1:265344/139‑1 (MQ=255)

                                             gACCGTAAATTCCCCCGCGCCCGCCAGCGCCATCGGTAGCACCAGTTGGTCAGCAAGATATT‑CCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACCTCTTTCACCAACTGTGCCGCAACCACCTCGGCACTGAcg                                                                         <  1:1296368/139‑1 (MQ=255)

                                                        cccccGCGCCCGCCAGCGCCATCGGTAGCACCAGTTGGGCAGCAAGATATT‑CCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACCTCTTTCACCAACTGTGCCGCAACCACCTCGGCACTGACGCGCTTTTCAcc                                                              <  1:66010/139‑1 (MQ=255)

                                                         ccccGCGCCCGCCAGCGCCATCGGTAGCACCAGTTGGTCAGCAAGATATT‑CCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACCTCTTTCACCAACTGTGCCGCAACCACCTCGGCACTGACGCGCTTTTCAcc                                                              <  1:381318/138‑1 (MQ=255)

                                                         ccccGCGCCCGCCAGCGCCATCGGTAGCACCAGTTGGTCAGCAAGATATT‑CCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACCTCTTTCACCAACTGTGCCGCAACCACCTCGGCACTGACGCGCTTTTCAcc                                                              >  2:381318/1‑138 (MQ=255)

                                                            cgcgCCCACCAGCGCCATCGGTAGCACCAGTTGGTCAGCAAGATATT‑CCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACCTCTTTCACCAACTGTGCCGCAACCACCTCGGCACTGACGCGCTTTTCACcgacg                                                          <  2:1148267/139‑1 (MQ=255)

                                                                   gccAGCGCCATCGGTAGCACCAGTTGGTCAGCAAGATATT‑CCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACCTCTTTCACCAACTGTGCCGCAACCACCTCGGCACTGACGCGCTTTTCACCGACGACaaaaa                                                   >  1:451955/1‑139 (MQ=255)

                                                                       gcgcCATCGGTAGCACCAGTTGGTCAGCAAGATATT‑CCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACCTCTTTCACCAACTGTGCCGCAACCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCg                                               <  1:1498836/139‑1 (MQ=255)

                                                                          ccATCGGTAGCACCAGTTGGTCAGCAAGATATT‑CCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACCTCTTTCACCAACTGTGCCGCAACCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTc                                            <  2:174861/139‑1 (MQ=255)

                                                                             tCGGTAGCACCAGTTGGTCAGCAAGATATT‑CCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACCTCTTTCACCAACTGTGCCGCAACCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGt                                         <  1:1501746/139‑1 (MQ=255)

                                                                                    cACCAGTTGGTCAGCAAGATATT‑CCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACCTCTTTCACCAACTGTGCCGCAACCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATAttt                                  >  1:312072/1‑139 (MQ=255)

                                                                                         gTTGGTCAGCAAGATATT‑CCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCAc                                                                                                                 <  1:1245883/55‑1 (MQ=255)

                                                                                         gTTGGTCAGCAAGATATT‑CCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCAc                                                                                                                 >  2:1245883/1‑55 (MQ=255)

                                                                                         gTTGGTCAGCAAGATATT‑CCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACCTCTTTCACCAACTGTGCCGCAACCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATAtttt                                 <  1:1078907/135‑1 (MQ=255)

                                                                                         gTTGGTCAGCAAGATATT‑CCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACCTCTTTCACCAACTGTGCCGCAACCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATAtttt                                 >  2:1078907/1‑135 (MQ=255)

                                                                                            ggTCAGCAAGATATT‑CCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACCTCTTTCACCAACTGTGCCGCAACCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTc                          <  1:278179/139‑1 (MQ=255)

                                                                                              tCAGCAAGATATT‑CCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCa                                                                                                                  <  2:124476/49‑1 (MQ=255)

                                                                                              tCAGCAAGATATT‑CCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCa                                                                                                                  >  1:124476/1‑49 (MQ=255)

                                                                                                        atT‑CCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCa                                                                                                                  <  2:949618/39‑1 (MQ=255)

                                                                                                        atT‑CCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCa                                                                                                                  >  1:949618/1‑39 (MQ=255)

                                                                                                        atT‑CCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACCTCTTTCACCAACTGTGCCGCAACCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCga              <  1:255289/139‑1 (MQ=255)

                                                                                                        atT‑CCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACCTCTTTCACCAACTGTGCCGCAACCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCga              >  1:139205/1‑139 (MQ=255)

                                                                                                          t‑CCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACCTCTTTCACCAACtgtg                                                                                                >  2:1523303/1‑55 (MQ=255)

                                                                                                          t‑CCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACCTCTTTCACCAACtgtg                                                                                                <  1:1523303/55‑1 (MQ=255)

                                                                                                          t‑CCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACCTCTTTCACCAACTGTGCCGCAACCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAg                 >  2:1288319/1‑134 (MQ=255)

                                                                                                          t‑CCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACCTCTTTCACCAACTGTGCCGCAACCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAg                 <  1:1288319/134‑1 (MQ=255)

                                                                                                          t‑CCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACCTCTTTCACCAACTGTGCCGCAACCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCgaga            <  2:139205/139‑1 (MQ=255)

                                                                                                             ccccACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACCTCTTTCACCAACTGTGCCGCAACCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACg          >  2:532348/1‑139 (MQ=255)

                                                                                                             ccccACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACCTCTTTCACCAACTGTGCCGCAACCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACg          >  2:783919/1‑139 (MQ=255)

                                                                                                                cACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACCTCTTTCAcc                                                                                                       >  2:1307189/1‑43 (MQ=255)

                                                                                                                cACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACCTCTTTCAcc                                                                                                       <  1:1307189/43‑1 (MQ=255)

                                                                                                                cACCGCCGCCGTGCGTGCCAGGTGGCGTTTCACCTCTTTCACCAACTGTGCCGCAACCACCTCGGCACTGACTCGCTTTTCACCGACGACAAAAAAGCGCTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTa       >  2:978538/1‑139 (MQ=255)

                                                                                                                     ccgccgTGCTTGCCAGGTGGCGTTTCACCTCTTTCACCAACTGTGCCGCAACCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTAcc  >  2:1449728/1‑139 (MQ=255)

                                                                                                                       gccgTGCTTGCCAGGTGGCGTTTCACCTCTTTCACCAACTGTGCCGCAACCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCg                                               <  1:161414/92‑1 (MQ=255)

                                                                                                                       gccgTGCTTGCCAGGTGGCGTTTCACCTCTTTCACCAACTGTGCCGCAACCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCg                                               >  2:161414/1‑92 (MQ=255)

CTCCACCACCGCGATATTGGTCAGCAGATGGCATGAGGGATGGGCGACCGTAAATTCCCCCGCGCCCGCCAGCGCCATCGGTAGCACCAGTTGGTCAGCAAGATATT‑CCCCCACCGCCGCCGTGCTTGCCAGGTAGCGTTTCACCTCTTTCACCAACTGTGCCGCAACCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACC  >  NC_000913/3555899‑3556153

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A