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
A12 F1 I2 R1	766	55.6	2631458	94.7%	2491990	109.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,083,620	G→A	R60C (CGT→TGT)	speB ←	agmatinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,083,620	0	G	A	100.0%	124.8 / NA	39	R60C (CGT→TGT)	speB	agmatinase
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (20/19); total (20/19)

TTCGCTCATCTCACGGGCATCGCCAAAGGCATATACCAGATCGCCGCAGTCCACGACGTTCAGACGCTCACGCATGTCGAAATTCCACGGGAAGCGGTTGTGTTCCCAGGCCAGATTCGTCGAAACCTGACGGATCGCTGCCGGACCGTGGCGACCACCCGCACGACCAGAAGTGGCCATATCGAACGGCACGCCAGTAATCACCCAGTCTGCATCGCTGTCATACGGCTGGAAGTTCATCGGCAGGCGTAAAAAACCAAAGG  >  NC_000913/3083489‑3083751

ttCGCTCATCTCACGGGCATCGCCAAAGGCATATACCAGATCGCCGCAGTCCACGACGTTCAGACGCTCACGCATGTCGAAATTCCACGGGAAGCGGTTGTGTTCCCAGGCCAGATTCGTCGAAACCTGACAGATCg                                                                                                                                >  1:769708/1‑137 (MQ=255)

ttCGCTCATCTCACGGGCATCGCCAAAGGCATATACCAGATCGCCGCAGTCCACGACGTTCAGACGCTCACGCATGTCGAAATTCCACGGGAAGCGGTTGTGTTCCCAGGCCAGATTCGTCGAAACCTGACAGATCg                                                                                                                                <  2:769708/137‑1 (MQ=255)

         ctcACGGGCATCGCCAAAGGCATATACCAGATCGCCGCAGTCCACGACGTTCAGACGCTCACGCATGTCGAAATTCCACGGGAAGCGGTTGTGTTCCCAGGCCAGATTCGTCGAAACCTGACAGATCGCTGCCGGACCg                                                                                                                     >  1:1104899/1‑139 (MQ=255)

                 cATCGCCAAAGGCATATACCAGATCGCCGCAGTCCACGACGTTCAGACGCTCACGCATGTCGAAATTCCACGGGAAGCGGTTGTGTTCCCAGGCCAGATTCGTCGAAACCTGACAGATCGCTGCCGGACCGTGGCGacc                                                                                                             <  2:6984/139‑1 (MQ=255)

                   tCGCCAAAGGCATATACCAGATCGCCGCAGTCCACGACGTTCAGACGCTCACGCATGTCGAAATTCCACGGGAAGCGGTTGTGTTCCCAGGCCAGATTCGTCGAAACCTGACAGATCGCTGCCGGACCGTGGCGaccac                                                                                                           >  2:283106/1‑139 (MQ=255)

                   tCGCCAAAGGCATATACCAGATCGCCGCAGTCCACGACGTTCAGACGCTCACGCATGTCGAAATTCCACGGGAAGCGGTTGTGTTCCCAGGCCAGATTCGTCGAAACCTGACAGATCGCTGCCGGACCGTGGCGaccac                                                                                                           >  1:537738/1‑139 (MQ=255)

                          aGGCATATACCAGATCGCCGCAGTCCACGACGTTCAGACGCTCACGCATGTCGAAATTCCACGGGAAGCGGTTGTGTTCCCAGGCCAGATTCGTCGAAACCTGACAGAt                                                                                                                                  >  1:76745/1‑109 (MQ=255)

                          aGGCATATACCAGATCGCCGCAGTCCACGACGTTCAGACGCTCACGCATGTCGAAATTCCACGGGAAGCGGTTGTGTTCCCAGGCCAGATTCGTCGAAACCTGACAGAt                                                                                                                                  <  2:76745/109‑1 (MQ=255)

                            gCATATACCAGATCGCCGCAGTCCACGACGTTCAGACGCTCACGCATGTCGAAATTCCACGGGAAGCGGTTGTGTTCCCAGGCCAGATTCGTCGAAACCTGACAGATCGCTGCCGGACCGTGGCGACCACCCGCACGAc                                                                                                  <  2:691029/139‑1 (MQ=255)

                              atatACCAGATCGCCGCAGTCCACGACGTTCAGACGCTCACGCATGTCGAAATTCCACGGGAAGCGGTTGTGTTCCCAGGCCAGATTCGTCGAAACCTGACAGAt                                                                                                                                  >  2:644605/1‑105 (MQ=255)

                              atatACCAGATCGCCGCAGTCCACGACGTTCAGACGCTCACGCATGTCGAAATTCCACGGGAAGCGGTTGTGTTCCCAGGCCAGATTCGTCGAAACCTGACAGAt                                                                                                                                  <  1:644605/105‑1 (MQ=255)

                                     aGATCGCCGCAGTCCACGACGTTCAGACGCTCACGCATGTCGAAATTCCACGGGAAGCGGTTGTGTTCCCAGGCCAGATTCGTCGAAACCTGACAGATCGCTGCCGGACCGTGGCGACCACCCGCACGACCAGAAGTgg                                                                                         >  2:78896/1‑139 (MQ=255)

                                      gATCGCCGCAGTCCACGACGTTCAGACGCTCACGCATGTCGAAATTCCACGGGAAGCGGTTGTGTTCCCAGGCCAGATTCGTCGAAACCTGACAGATCGCTGCCGGACCGTGGCGACCACCCGCACGACCAGAAGTGGc                                                                                        <  1:419310/139‑1 (MQ=255)

                                       aTCGCCGCAGTCCACGACGTTCAGACGCTCACGCATGTCGAAATTCCACGGGAAGCGGTTGTGTTCCCAGGCCAGATTCGTCGAAACCTGACAGATCGCTGCCGGACCGTGGCGACCACCCGCACGACCAGAAGTGGcc                                                                                       >  2:557532/1‑139 (MQ=255)

                                       aTCGCCGCAGTCCACGACGTTCAGACGCTCACGCATGTCGAAATTCCACGGGAAGCGGTTGTGTTCCCAGGCCAGATTCGTCGAAACCTGACAGATCGCTGCCGGACCGTGGCGACCACCCGCACGACCAGAAGTGGcc                                                                                       >  2:1181205/1‑139 (MQ=255)

                                         cgccgcAGTCCACGACGTTCAGACGCTCACGCATGTCGAAATTCCACGGGAAGCGGTTGTGTTCCCAGGCCAGATTCGTCGAAACCTGACAGATCGCTGCCGGACCGTGGCGACCACCCGCACGACCAGAAGTGGCCat                                                                                     >  2:1208909/1‑139 (MQ=255)

                                           ccgcAGTCCACGACGTTCAGACGCTCACGCATGTCGAAATTCCACGGGAAGCGGTTGTGTTCCCAGGCCAGATTCGTCGAAACCTGACAGATCGCTGCCGGACCGTGGCGACCACCCGCACGACCAGAAGTgg                                                                                         >  1:776499/1‑133 (MQ=255)

                                           ccgcAGTCCACGACGTTCAGACGCTCACGCATGTCGAAATTCCACGGGAAGCGGTTGTGTTCCCAGGCCAGATTCGTCGAAACCTGACAGATCGCTGCCGGACCGTGGCGACCACCCGCACGACCAGAAGTgg                                                                                         <  2:776499/133‑1 (MQ=255)

                                            cgcAGTCCACGACGTTCAGACGCTCACGCATGTCGAAATTCCACGGGAAGCGGTTGTGTTCCCAGGCCAGATTCGTCGAAACCTGACAGATCGCTGCCGGACCGTGGCGACCACCCGCACGACCAGAAGTGGCCATATc                                                                                  >  2:979602/1‑139 (MQ=255)

                                             gcAGTCCACGACGTTCAGACGCTCACGCATGTCGAAATTCCACGGGAAGCGGTTGTGTTCCCAGGCCAGATTCGTCGAAACCTGACAGATCGCTGCCGGACCGTGGCGACCACCCGCACGACCAGAAGTGGCCATATCg                                                                                 <  1:557532/139‑1 (MQ=255)

                                                    acgacgTTCAGACGCTCACGCATGTCGAAATTCCACGGGAAGCGGTTGTGTTCCCAGGCCAGATTCGTCGAAACCTGACAGATCGCTGCCGGACCGTGGCGACCACCCGCACGACCAGAAGTGGCCATATCGAACGGCa                                                                          <  1:1314977/139‑1 (MQ=255)

                                                        cgTTCAGACGCTCACGCATGTCGAAATTCCACGGGAAGCGGTTGTGTTCCCAGGCCAGATTCGTCGAAACCTGACAGATCGCTGCCGGACCGTGGCGACCACCCGCACGACCAGAAGTGGCCATATCGACCGGCACGcc                                                                      <  1:1241786/139‑1 (MQ=255)

                                                                      cGCATGTCGAAATTCCACGGGAAGCGGTTGTGTTCCCAGGCCAGATTCGTCGAAACCTGACAGATCGCTGCCGGATCGTGGCGACCACCCGCACGACCAGAAGTGGCCATATCGAACGGCACGCCAGTAATCACCCAGt                                                        <  2:856668/139‑1 (MQ=255)

                                                                            tCGAAATTCCACGGGAAGCGGTTGTGTTCCCAGGCCAGATTCGTCGAAACCTGACAGATCGCTGCCGGACCGTGGCGACCACCCGCACGACCAGAAGTGGCCATATCGAACGGCACGCCAGTAATCACCCAGTCTGCAt                                                  <  2:473481/139‑1 (MQ=255)

                                                                                           aaGCGGTTGTGTTCCCAGGCCAGATTCGTCGAAACCTGACAGATCGCTGCCGGACCGTGGCGACCACCCGCa                                                                                                      <  1:260367/72‑1 (MQ=255)

                                                                                           aaGCGGTTGTGTTCCCAGGCCAGATTCGTCGAAACCTGACAGATCGCTGCCGGACCGTGGCGACCACCCGCa                                                                                                      >  2:260367/1‑72 (MQ=255)

                                                                                               ggTTGTGTTCCCAGGCCAGATTCGTCGAAACCTGACAGATCGCTGCCGGACCGTGGCGACCACCCGCACGACCAGAAGTGGCCATATCGAACGGCACGCCAGTAATCACCCAGTCTGCATCGCTGTCATa                                        >  2:1254215/1‑130 (MQ=255)

                                                                                               ggTTGTGTTCCCAGGCCAGATTCGTCGAAACCTGACAGATCGCTGCCGGACCGTGGCGACCACCCGCACGACCAGAAGTGGCCATATCGAACGGCACGCCAGTAATCACCCAGTCTGCATCGCTGTCATa                                        <  1:1254215/130‑1 (MQ=255)

                                                                                                gTTGTGTTCCCAGGCCAGATTCGTCGAAACCTGACAGAt                                                                                                                                  >  2:168906/1‑39 (MQ=255)

                                                                                                gTTGTGTTCCCAGGCCAGATTCGTCGAAACCTGACAGAt                                                                                                                                  <  1:168906/39‑1 (MQ=255)

                                                                                                    tgtTCCCAGGCCAGATTCGTCGAAACCTGACAGATCGCTGCCGGACCGTGGCGACCACCCGCACGACCAGAAGTGGCCATATCGAACGGCACGCCAGTAATCACCCAGTCTGCATCGCTGTCATACGGCTGGAAGTTCa                          >  2:178603/1‑139 (MQ=255)

                                                                                                                  aTTCGTCGAAACCTGACAGATCGCTGCCGGACCGTGGCGACCACCCGCACGACCAGAAGTGGCCATATCGAACGGCACGCCAGTAATCACCCAGTCTGCATCGCTGTCATACGGCTGGAAGTTCATCGGCAGGCGTaaa            >  2:275714/1‑139 (MQ=255)

                                                                                                                  aTTCGTCGAAACCTGACAGATCGCTGCCGGACCGTGGCGACCACCCGCACGACCAGAAGTGGCCATATCGAACGGCACGCCAGTAATCACCCAGTCTGCATCGCTGTCATACGGCTGGAAGTTCATCGGCAGGCGTaaa            <  1:1200256/139‑1 (MQ=255)

                                                                                                                       tcgAAACCTGACAGATCGCTGCCGGACCGTGGCGACCACCCGCACGACCAGAAGTGGCCatat                                                                                   >  2:224753/1‑63 (MQ=255)

                                                                                                                       tcgAAACCTGACAGATCGCTGCCGGACCGTGGCGACCACCCGCACGACCAGAAGTGGCCatat                                                                                   <  1:224753/63‑1 (MQ=255)

                                                                                                                       tcgAAACCTGACAGATCGCTGCCGGACCGTGGCGACCACCCGCACGACCAGAAGTGGCCATATCGAACGGCACGCCAGTAATCACCCAGTCTGCATCGCTGTCATACGGCTGGAAGTTCATCGGCAGGCGTAAAAAAcc       >  2:872200/1‑139 (MQ=255)

                                                                                                                            aCCTGACAGATCGCTGCCGGACCGTGGCGACCACCCGCACGACCAGAAGTGGCCATATCGAACGGCACGCCAGTAATCACCCAGTCTg                                                     <  2:1236868/88‑1 (MQ=255)

                                                                                                                            aCCTGACAGATCGCTGCCGGACCGTGGCGACCACCCGCACGACCAGAAGTGGCCATATCGAACGGCACGCCAGTAATCACCCAGTCTg                                                     >  1:1236868/1‑88 (MQ=255)

                                                                                                                            aCCTGACAGATCGCTGCCGGACCGTGGCGACCACCCGCACGACCAGAAGTGGCCATATCGAACGGCACGCCAGTAATCACCCAGTCTGCATCGCTGTCATACGGCTGGAAGTTCATCGGCAGGCGTAAAAAACCAAAgg  <  2:282484/139‑1 (MQ=255)

TTCGCTCATCTCACGGGCATCGCCAAAGGCATATACCAGATCGCCGCAGTCCACGACGTTCAGACGCTCACGCATGTCGAAATTCCACGGGAAGCGGTTGTGTTCCCAGGCCAGATTCGTCGAAACCTGACGGATCGCTGCCGGACCGTGGCGACCACCCGCACGACCAGAAGTGGCCATATCGAACGGCACGCCAGTAATCACCCAGTCTGCATCGCTGTCATACGGCTGGAAGTTCATCGGCAGGCGTAAAAAACCAAAGG  >  NC_000913/3083489‑3083751

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