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
A3 F1 I2 R1	777	59.2	2955938	92.5%	2734242	106.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,380,807	G→A	220 (TAG→TAA)	ycjU →	beta‑phosphoglucomutase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,380,807	0	G	A	100.0%	120.2 / NA	38	220 (TAG→TAA)	ycjU	beta‑phosphoglucomutase
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (21/17); total (21/17)

CGGGCATTGACGCCATTAACGCCAGCGGTATGCGCTCGGTGGGGATCGGCGCGGGCTTAACCGGGGCGCAATTACTGTTGCCTTCAACGGAATCACTCACCTGGCCGCGGTTATCGGCCTTCTGGCAAAACGTATAGCAAAGGAATCAACATGGCTCAGCTTTCGTTACAACATATTCAAAAAATCTACGATAACCAGGTGCATGTGGTGAAGGACTTCAACCTGGAAATTGCCGATAAAGAGTTCATCGTGTTTGTCGGCCCGTCGGGC  >  NC_000913/1380671‑1380940

cGGGCATTGACGCCAGTAACGCCAGCGGTATGCGCTCGGTGGGGATCGGCGCGGGCTTAACCGGGGCGCAATTACTGTTGCCTTCAACGGAATCACTCACCTGGCCGCGGTTATCGGCCTTCTGGCAAAACGTATAACa                                                                                                                                     <  1:892637/139‑1 (MQ=255)

 gggCATTGACGCCATTAACGCCAGCGGTATGCGCTCGGTGGGGATCGGCGCGGGCTTAACCGGGGCGCAATTACTGTTGCCTTCAACGGAATCACTCACCTGGCCGCGGTTATCGGCCTTCTGGCAAAACGTATAACaa                                                                                                                                    <  2:351257/139‑1 (MQ=255)

  ggCATTGACGCCATTAACGCCAGCGGTATGCGCTCGGTGGGGATCGGCGCGGGCTTAACCGGGGCGCAATTACTGTTGCCTTCAACGGAATCACTCACCTGGCCGCGGTTATCGGCCTTCTGGCAAAACGTATAACaaa                                                                                                                                   <  2:635492/139‑1 (MQ=255)

      ttGACGCCATTAACGCCAGCGGTATGCGCTCGGTGGGGATCGGCGCGGGCTTAACCGGGGCGCAATTACTGTTGCCTTCAACGGAATCACTCACCTGGCCGCGGTTATCGGCCTTCTGGCAAAACGTATAACAAAGGaa                                                                                                                               >  2:1053898/1‑139 (MQ=255)

                         cGGTATGCGCTCGGTGGGGATCGGCGCGGGCTTAACCGGGGCGCAATTACTGTTGCCTTCAACGGAATCACTCACCTGGCCGCGGTTATCGGCCTTCTGGCAAAACGTATAACAAAGGAATCAACATGGCTCAGCTTTc                                                                                                            >  2:1139023/1‑139 (MQ=255)

                                     ggTGGGGATCGGCGCGGGCTTAACCGGGGCGCAATTACTGTTGCCTTCAACGGAATCACTCACCTGGCCGCGGTTATCGGCCTTCTGGCAAAACGTATAACAAAGGAATCAACATGGCTCAGCTTTCGTTACAACatat                                                                                                >  1:994643/1‑139 (MQ=255)

                                               ggCGCGGGCTTAACCGGGGCGCAATTACTGTTGCCTTCAACGGAATCACTCACCTGGCCGCGGTTATCGGCCTTCTGGCAAAACGTATAACAAAGGAATCAACATGGCTCAGCTTTCGTTACAACATATTCAAAAAATc                                                                                      >  1:291564/1‑139 (MQ=255)

                                                           aCCGGGGCGCAATTACTGTTGCCTTCAACGGAATCACTCACCTGGCCGCGGTTATCGGCCTTCTGGCAAAACGTATAACAAAGGAATCAACATGGCTCAGCTTTCGTTACAACATATTCAAAAAATCTACGATAACCAg                                                                          >  1:1381661/1‑139 (MQ=255)

                                                            ccGGGGCGCAATTACTGTTGCCTTCAACGGAATCACTCACCTGGCCGCGGTTATCGGCCTTCTGGCAAAACGTATAACAAAGGAATCAACATGGCTCAGCTTTCGTTACAACATATTCAAAAAATCTACGATAACCAgg                                                                         <  1:1053898/139‑1 (MQ=255)

                                                                ggCGCAATTACTGTTGCCTTCAACGGAATCACTCACCTGGCCGCGGTTATCGGCCTTCTGGCAAAACGTATAACAAAGGAAt                                                                                                                              <  2:365513/82‑1 (MQ=255)

                                                                ggCGCAATTACTGTTGCCTTCAACGGAATCACTCACCTGGCCGCGGTTATCGGCCTTCTGGCAAAACGTATAACAAAGGAAt                                                                                                                              >  1:365513/1‑82 (MQ=255)

                                                                ggCGCAATTACTGTTGCCTTCAACGGAATCACTCACCTGGCCGCGGTTATCGGCCTTCTGGCAAAACGTATAACAAAGGAATCAACATGGCTCAGCttt                                                                                                             <  2:861160/99‑1 (MQ=255)

                                                                ggCGCAATTACTGTTGCCTTCAACGGAATCACTCACCTGGCCGCGGTTATCGGCCTTCTGGCAAAACGTATAACAAAGGAATCAACATGGCTCAGCttt                                                                                                             >  1:861160/1‑99 (MQ=255)

                                                                ggCGCAATTACTGTTGCCTTCAACGGAATCACTCACCTGGCCGCGGTTATCGGCCTTCTGGCAAAACGTATAACAAAGGAATCAACATGGCTCAGCTTTCGTTACAACATATTCAAAAAATCTACGATAACCAGGTGCa                                                                     <  2:965363/139‑1 (MQ=255)

                                                                ggCGCAATTACTGTTGCCTTCAACGGAATCACTCACCTGGCCGCGGTTATCGGCCTTCTGGCAAAACGTATAACAAAGGAATCAACATGGCTCAGCTTTCGTTACAACATATTCAAAAAATCTACGATAACCAGGTGCa                                                                     >  1:89217/1‑139 (MQ=255)

                                                                ggCGCAATTACTGTTGCCTTCAACGGAATCACTCACCTGGCCGCGGTTATCGGCCTTCTGGCAAAACGTATAACAAAGGAATCAACATGGCTCAGCTTTCGTTACAACATATTCAAAAAATCTACGATAACCAGGTGCa                                                                     <  2:1381661/139‑1 (MQ=255)

                                                                  cgcAATTACTGTTGCCTTCAACGGAATCACTCACCTGGCCGCGGTTATCGGCCTTCTGGCAAAACGTATAACAAAGGAATCAACATGGCTCAGCTTTCGTTACAACATATTCAAAAAATCTACGATAACCAGGTGCAtg                                                                   <  2:255623/139‑1 (MQ=255)

                                                                    cAATTACTGTTGCCTTCAACGGAATCACTCACCTGGCCGCGGTTATCGGCCTTCTGGCAAAACGTATAACAAAGGAATCAACATGGCTCAGCTTTCGTTACAACATATTCAAAAAATCTACGATAACCAGGTGCAtgtg                                                                 >  2:330332/1‑139 (MQ=255)

                                                                       ttACTGTTGCCTTCAACGGAATCACTCACCTGGCCGCGGTTATCGGCCTTCTGGCAAAACGTATAACAAAGGAAt                                                                                                                              >  2:1060384/1‑75 (MQ=255)

                                                                       ttACTGTTGCCTTCAACGGAATCACTCACCTGGCCGCGGTTATCGGCCTTCTGGCAAAACGTATAACAAAGGAAt                                                                                                                              <  1:1060384/75‑1 (MQ=255)

                                                                             ttGCCTTCAACGGAATCACTCACCTGGCCGCGGTTATCGGCCTTCTGGCAAAACGTATAACAAAGGAATCaa                                                                                                                           >  2:608392/1‑72 (MQ=255)

                                                                             ttGCCTTCAACGGAATCACTCACCTGGCCGCGGTTATCGGCCTTCTGGCAAAACGTATAACAAAGGAATCaa                                                                                                                           <  1:608392/72‑1 (MQ=255)

                                                                               gCCTTCAACGGAATCACTCACCTGGCCGCGGTTATCGGCCTTCTGGCAAAACGTATAACAAAGGAATCAACATGGCTCAGCTTTCGTTACAACATATTCAAAAAATCTACGATAACCAGGTGCATGTGGTGAAGGACtt                                                      >  1:336594/1‑139 (MQ=255)

                                                                                          aaTCACTCACCTGGCCGCGGTTATCGGCCTTCTGGCAAAACGTATAACAAAGGAATCAACATGGCTCAGCTTTCGTTACAACATATTCAAAAAATCTACGATAACCAGGTGCATGTGGTGAAGGACTTCAACCTGGaaa                                           >  1:361210/1‑139 (MQ=255)

                                                                                                 cacCTGGCCGCGGTTATCGGCCTTCTGGCAAAACGTATAACAAAGGAATCAACATGGCTCAGCTTTCGTTACAACATATTCAAAAAATCTACGATAACCAGGTGCa                                                                     <  2:288620/106‑1 (MQ=255)

                                                                                                 cacCTGGCCGCGGTTATCGGCCTTCTGGCAAAACGTATAACAAAGGAATCAACATGGCTCAGCTTTCGTTACAACATATTCAAAAAATCTACGATAACCAGGTGCa                                                                     >  1:288620/1‑106 (MQ=255)

                                                                                                    cTGGCCGCGGTTATCGGCCTTCTGGCAAAACGTATAACAAAGGAATCAACATGGCTCAGCtt                                                                                                              <  1:751334/62‑1 (MQ=255)

                                                                                                    cTGGCCGCGGTTATCGGCCTTCTGGCAAAACGTATAACAAAGGAATCAACATGGCTCAGCtt                                                                                                              >  2:751334/1‑62 (MQ=255)

                                                                                                    cTGGCCGCGGTTATCGGCCTTCTGGCAAAACGTATAACAAAGGAATCAACATGGCTCAGCTTTCGTTACAACATATTCAAAAAATCTACGATAACCAGGTGCATGTGGTGAAGGACTTCAACCTGGAAATTGCCGATaa                                 >  1:861356/1‑139 (MQ=255)

                                                                                                      ggCCGCGGTTATCGGCCTTCTGGCAAAACGTATAACAAAGGAGTCAACATGGCTCAGCTTTCGTTACAACATATTCAAAAAATCTACGATAACCAGGTGCATGTGGTGAAGGACTTCAACCGTGAAATTGCCGATaaaa                               >  1:461971/1‑138 (MQ=255)

                                                                                                       gCCGCGGTTATCGGCCTTCTGGCAAAACGTATAACAAAGGAATCAACATGGCTCAGCTTTCGTTACAACATATTCAAAAAATCTACGATAACCAGGTGCATGTGGTGAAGGACTTCAACCTGGAAATTGCCGATAAaga                              >  2:711217/1‑139 (MQ=255)

                                                                                                         cgcgGTTATCGGCCTTCTGGCAAAACGTATAACAAAGGAATCAACATGGCTCAGCTTTCGTTACAACATATTCAAAAAATCTACg                                                                                  <  1:896292/85‑1 (MQ=255)

                                                                                                         cgcgGTTATCGGCCTTCTGGCAAAACGTATAACAAAGGAACCAACATGGCTCAGCTTTCGTTACAACATATTCAAAAAATCTACg                                                                                  >  2:896292/1‑85 (MQ=255)

                                                                                                            ggTTATCGGCCTTCTGGCAAAACGTATAACAAAGGAATCAACATGGCTCAGCTTTCGTTACAACATATTCAAAAAATCTACGATAACCAGGTGCATGTGGTGAAGGACTTCAACCTGGAAATTGCCGATAAAGAGTTCa                         <  2:336594/139‑1 (MQ=255)

                                                                                                            ggTTATCGGCCTTCTGGCAAAACGTATAACAAAGGAATCAACATGGCTCAGCTTTCGTTACAACATATTCAAAAAATCTACGATAACCAGGTGCATGTGGTGAAGGACTTCAACCTGGAAATTGCCGATAAAGAGTTCa                         <  2:361210/139‑1 (MQ=255)

                                                                                                                 tCGGCCTTCTGGCAAAACGTATAACAAAGGAATCAACATGGCTCAGCt                                                                                                               >  2:1422948/1‑48 (MQ=255)

                                                                                                                 tCGGCCTTCTGGCAAAACGTATAACAAAGGAATCAACATGGCTCAGCt                                                                                                               <  1:1422948/48‑1 (MQ=255)

                                                                                                                                   gTATAACAAAGGAATCAACATGGCTCAGCTTTCGTTACAACATATTCAAAAAATCTACGATAACCAGGTGCATGTGGTGAAGGACTTCAACCTGGAAATTGCCGATAAAGAGTTCATCGTGTTTGTCGGCCCGTCGGGc  >  2:1132758/1‑139 (MQ=255)

CGGGCATTGACGCCATTAACGCCAGCGGTATGCGCTCGGTGGGGATCGGCGCGGGCTTAACCGGGGCGCAATTACTGTTGCCTTCAACGGAATCACTCACCTGGCCGCGGTTATCGGCCTTCTGGCAAAACGTATAGCAAAGGAATCAACATGGCTCAGCTTTCGTTACAACATATTCAAAAAATCTACGATAACCAGGTGCATGTGGTGAAGGACTTCAACCTGGAAATTGCCGATAAAGAGTTCATCGTGTTTGTCGGCCCGTCGGGC  >  NC_000913/1380671‑1380940

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A