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
A6 F1 I2 R1	758	59.3	2864096	93.9%	2689386	105.7

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%	128.8 / NA	37	Y273H (TAC→CAC)	rtcA	RNA 3'‑terminal phosphate cyclase
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (14/23); total (14/23)

CTCCACCACCGCGATATTGGTCAGCAGATGGCATGAGGGATGGGCGACCGTAAATTCCCCCGCGCCCGCCAGCGCCATCGGTAGCACCAGTTGGTCAGCAAGATATTCCCCCACCGCCGCCGTGCTTGCCAGGTAGCGTTTCACCTCTTTCACCAACTGTGCCGCAACCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACC  >  NC_000913/3555899‑3556153

cTCCACCACCGCGATATTGGTCAGCAGATGGCATGAGGGATGGGCGACCGTAAATTCCCCCGCGCCCGCCAGCGCCATCGGTAGCACCAGTTGGTCAGCAAGATATTCCCCCACCGCCGCCGTGCTTGCCAGGTGGCGt                                                                                                                      >  2:612735/1‑139 (MQ=255)

    accaccGCGATATTGGTCAGCAGATGGCATGAGGGATGGGCGACCGTAAATTCCCCCGCGCCCGCCAGCGCCATCGGTAGCACCAGTTGGTCAGCAAGATATTCCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCa                                                                                                                  <  1:985736/139‑1 (MQ=255)

      caccGCGATATTGGTCAGCAGATGGCATGAGGGATGGGCGACCGTAAATTCCCCCGCGCCCGCCAGCGCCATCGGTAGCACCAGTTGGTCAGCAAGATATTCCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCAcc                                                                                                                <  2:119910/139‑1 (MQ=255)

         cgcgATATTGGTCAGCAGATGGCATGAGGGATGGGCGACCGTAAATTCCCCCGCGCCCGCCAGCGCCATCGGTAGCACCAGTTGGTCAGCAAGATATTCCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACctct                                                                                                             >  2:112509/1‑139 (MQ=255)

           cgATATTGGTCAGCAGATGGCATGAGGGATGGGCGACCGTAAATTCCCCCGCGCCCGCCAGCGCCATCGGTAGCACCAGTTGGTCAGCAAGATATTCCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACCTCttt                                                                                                           >  1:1289272/1‑139 (MQ=255)

               atTGGTCAGCAGATGGCATGAGGGATGGGCGACCGTAAATTCCCCCGCGCCCGCCAGCGCCATCGGTAGCACCAGTTGGTCAGCAAGATATTCCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACCTCTTTCAcc                                                                                                       <  2:806815/139‑1 (MQ=255)

                          gATGGCATGAGGGATGGGCGACCGTAAATTCCCCCGCGCCCGCCAGCGCCATCGGTAGCACCAGTTGGTCAGCAAGATATTCCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACCTCTTTCACCAACTGTGCCGc                                                                                            <  2:66207/139‑1 (MQ=255)

                             ggCATGAGGGATGGGCGACCGTAAATTCCCCCGCGCCCGCCAGCGCCATCGGTAGCACCAGTTGGTCAGCAAGATATTCCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACCTCTTTCACCAACTGTGCCGCAac                                                                                         <  1:112509/139‑1 (MQ=255)

                             ggCATGAGGGATGGGCGACCGTAAATTCCCCCGCGCCCGCCAGCGCCATCGGTAGCACCAGTTGGTCAGCAAGATATTCCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACCTCTTTCACCAACTGTGCCGCAac                                                                                         >  1:1162450/1‑139 (MQ=255)

                             ggCATGAGGGATGGGCGACCGTAAATTCCCCCGCGCCCGCCAGCGCCATCGGTAGCACCAGTTGGTCAGCAAGATATTCCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACCTCTTTCACCAACTGTGCCGCAac                                                                                         <  1:1297936/139‑1 (MQ=255)

                             ggCATGAGGGATGGGCAACCGTAAATTCCCCCGCGCCCGCCAGCGCCATCGGTAGCACCAGTTGGTCAGCAAGATATTCCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACCTCTTTCACCAACTGTGCCGCAac                                                                                         <  1:1115983/139‑1 (MQ=255)

                               cATGAGGGATGGGCGACCGTAAATTCCCCCGCGCCCGCCAGCGCCATCGGTAGCACCAGTTGGTCAGCAAGATATTCCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACCTCTTTCACCAACTGTGCCGCAacca                                                                                       >  1:812188/1‑139 (MQ=255)

                                  gAGGGATGGGCGACCGTAAATTCCCCCGCGCCCGCCAGCGCCATCGGTAGCACCAGTTGGTCAGCAAGATATTCCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACCTCTTTCACCAACTGTGCCGCAACCACCt                                                                                    <  1:1350830/139‑1 (MQ=255)

                                  gAGGGATGGGCGACCGTAAATTCCCCCGCGCCCACCAGCGCCATCGGTAGCACCAGTTGGTCAGCAAGATATTCCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCAc                                                                                                                 <  1:640353/110‑1 (MQ=255)

                                  gAGGGATGGGCGACCGTAAATTCCCCCGCGCCCACCAGCGCCATCGGTAGCACCAGTTGGTCAGCAAGATATTCCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCAc                                                                                                                 >  2:640353/1‑110 (MQ=255)

                                             gACCGTAAATTCCCCCGCGCCCGCCAGCGCCATCGGTAGCACCAGTTGGTCAGCAAGATATTCCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACCTCTTTCACCAACTGTGCCGCAACCACCTCGGCACTGAcg                                                                         <  1:612735/139‑1 (MQ=255)

                                             gACCGTAAATTCCCCCGCGCCCGCCAGCGCCATCGGTAGCACCAGTTGGTCAGCAAGATATTCCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACCTCTTTCACCAACTGTGCCGCAACCACCTCGGCACTGAcg                                                                         <  1:545955/139‑1 (MQ=255)

                                              aCCGTAAATTCCCCCGCGCCCGCCAGCGCCATCGGTAGCACCAGTTGGTCAGCAAGATATTCCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACct                                                                                                               >  1:1012197/1‑100 (MQ=255)

                                              aCCGTAAATTCCCCCGCGCCCGCCAGCGCCATCGGTAGCACCAGTTGGTCAGCAAGATATTCCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACct                                                                                                               <  2:1012197/100‑1 (MQ=255)

                                                cGTAAATTCCCCCGCGCCCGCCAGCGCCATCGGTAGCACCAGTTGGTCAGCAAGATATTCCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCAc                                                                                                                 >  1:915385/1‑96 (MQ=255)

                                                cGTAAATTCCCCCGCGCCCGCCAGCGCCATCGGTAGCACCAGTTGGTCAGCAAGATATTCCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCAc                                                                                                                 <  2:915385/96‑1 (MQ=255)

                                                         ccccGCGCCCGCCAGCGCCATCGGTAGCACCAGTTGGTCAGCAAGATATTCCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACCTCTTTCACCAACTGTGCCGCAACCACCTCGGCACTGACGCGCTTTTCACcg                                                             >  2:892648/1‑139 (MQ=255)

                                                                              cGGTAGCACCAGTTGGTCAGCAAGATATTCCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACCTCTTTCACCAACTGTGCCGCAACCACCTCGGCACTGACGCGCTTTTCAcc                                                              <  2:1243984/117‑1 (MQ=255)

                                                                              cGGTAGCACCAGTTGGTCAGCAAGATATTCCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACCTCTTTCACCAACTGTGCCGCAACCACCTCGGCACTGACGCGCTTTTCAcc                                                              >  1:1243984/1‑117 (MQ=255)

                                                                                  aGCACCAGTTGGTCAGCAAGATATTCCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACCTCTTTCACCAACTGTGCCGCAACCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGt                                         >  1:732102/1‑134 (MQ=255)

                                                                                  aGCACCAGTTGGTCAGCAAGATATTCCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACCTCTTTCACCAACTGTGCCGCAACCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGt                                         <  2:732102/134‑1 (MQ=255)

                                                                                    cACCAGTTGGTCAGCAAGATATTCCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACctct                                                                                                             <  1:613199/64‑1 (MQ=255)

                                                                                    cACCAGTTGGTCAGCAAGATATTCCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACctct                                                                                                             >  2:613199/1‑64 (MQ=255)

                                                                                           tGGTCAGCAAGATATTCCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACCTCTTTCACCAACTGTGCCGCAac                                                                                         >  1:992654/1‑77 (MQ=255)

                                                                                           tGGTCAGCAAGATATTCCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACCTCTTTCACCAACTGTGCCGCAac                                                                                         <  2:992654/77‑1 (MQ=255)

                                                                                                         ttCCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACCTCTTTCACCAACTGTGCCGCAACCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCgag             <  2:1162450/139‑1 (MQ=255)

                                                                                                         ttCCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACCTCTTTCACCAACTGTGCCGCAACCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCgag             <  2:1289272/139‑1 (MQ=255)

                                                                                                         ttCCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACCTCTTTCACCAACTGTGCCGCAACCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCgag             <  1:1321756/139‑1 (MQ=255)

                                                                                                          tCCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACCTCTTTCACCAACTGTGCCGCAACCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACt                      <  2:1344149/129‑1 (MQ=255)

                                                                                                          tCCCCCACCGCCGCCGTGCTTGCCAGGTGGCGTTTCACCTCTTTCACCAACTGTGCCGCAACCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACt                      >  1:1344149/1‑129 (MQ=255)

                                                                                                                    ccgccgTGCTTGCCAGGTGGCGTTTCACCTCTTTCACCAACTGTGCCGCAACCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTAcc  <  1:820997/139‑1 (MQ=255)

                                                                                                                    ccgccgTGCTTGCCAGGTGGCGTTTCACCTCTTTCACCAACTGTGCCGCAACCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTAcc  <  1:1158054/139‑1 (MQ=255)

CTCCACCACCGCGATATTGGTCAGCAGATGGCATGAGGGATGGGCGACCGTAAATTCCCCCGCGCCCGCCAGCGCCATCGGTAGCACCAGTTGGTCAGCAAGATATTCCCCCACCGCCGCCGTGCTTGCCAGGTAGCGTTTCACCTCTTTCACCAACTGTGCCGCAACCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACC  >  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