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
A1 F1 I2 R1	765	46.1	2269152	93.8%	2128464	105.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,333,691	A→G	pseudogene (712/4605 nt)	yfaS ←	pseudogene, bacterial alpha2‑macroglobulin YfaS variant family, putative membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,333,691	0	A	G	100.0%	158.7 / NA	45	pseudogene (712/4605 nt)	yfaS	pseudogene, bacterial alpha2‑macroglobulin YfaS variant family, putative membrane protein
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (20/25); total (20/25)

GGCTTCGCTTCACCCTGTTTTTTACCCGCGGTCCACACCAGAAGCTCTTTGCCTGACACTTTGCTAAGCGCCACGGTATCGGAAACAAACACCACCGTCGTCGCCCGATACCCACCAACCATCGCCTCGACGAGGTACAGTCCCGGCTCTTGTTGGCCGAGAGGAATATAAATGTTACCCGGCTGCGGCGAGATGAAATTGCTGGATGCGCCTTCCAGTTTTACCCCTTGCTGCGGCTCGAACGGTTTAGCCTGCCATAGTGGATAACGGA  >  NC_000913/2333555‑2333825

ggCTTCGCTTCACCCTGTTTTTTACCCGCGGTCCACACCAGAAGCTCTTTGCCTGACACTTTGCTAAGCGCCACGGTATCGGAAACAAACACCACCGTCGTCGCCCGATACCCACCAACCATCGCCTCGACGAGGTGCa                                                                                                                                      >  2:632866/1‑139 (MQ=255)

          cACCCTGTTTTTTACCCGCGGTCCACACCAGAAGCTCTTTGCCTGACACTTTGCTAAGCGCCACGGTATCGGAAACAAACACCACCGTCGTCGCCCGATACCCACCAACCATCGCCTCGACGAGGTGCAGTCCCGGctc                                                                                                                            >  2:1064574/1‑139 (MQ=255)

                   ttttACCCGCGGTCCACACCAGAAGCTCTTTGCCTGACACTTTGCTAAGCGCCACGGTATCGGAAACAAACACCACCGTCGTCGCCCGATACCCACCAACCATCGCCTCGACGAGGTGCAGTCCCGGCTCTTGTTGGcc                                                                                                                   <  1:152752/139‑1 (MQ=255)

                      tACCCGCGGTCCACACCAGAAGCTCTTTGCCTGACACTTTGCTAAGCGCCACGGTATCGGAAACAAACACCACCGTCGTCGCCCGATACCCACCAACCATCGCCTCGACGAGGTGCAGTCCCGGCTCTTGTTGGCCgag                                                                                                                <  1:806440/139‑1 (MQ=255)

                        cccGCGGTCCACACCAGAAGCTCTATGCCTGACACTTTGCTAAGCGCCACGGTATCGGAAACAAACACCACCGTCGTCGCCCGATACCCACCAACCATCGCCTCGACGAGGTGCAGTCCCGGCTCTTGTTGGCCGagag                                                                                                              <  1:632866/139‑1 (MQ=255)

                           gcgGTCCACACCAGAAGCTCTTTGCCTGACACTTTGCTAAGCGCCACGGTATCGGAAACAAACACCACCGTCGTCGCCCGATACCCACCAACCATCGCCTCGACGAGGTGCAGTCCCGGCTCTTGTTGGCCgag                                                                                                                >  1:459264/1‑134 (MQ=255)

                           gcgGTCCACACCAGAAGCTCTTTGCCTGACACTTTGCTAAGCGCCACGGTATCGGAAACAAACACCACCGTCGTCGCCCGATACCCACCAACCATCGCCTCGACGAGGTGCAGTCCCGGCTCTTGTTGGCCgag                                                                                                                <  2:459264/134‑1 (MQ=255)

                           gcgGTCCACACCAGAAGCTCTTTGCCTGACACTTTGCTAAGCGCCACGGTATCGGAAACAAACACCACCGTCGTCGCCCGATACCCACCAACCATCGCCTCGACGAGGTGCAGTCCCGGCTCTTGTTGGCCGAGAGGaa                                                                                                           >  2:951818/1‑139 (MQ=255)

                           gcgGTCCACACCAGAAGCTCTTTGCCTGACACTTTGCTAAGCGCCACGGTATCGGAAACAAACACCACCGTCGTCGCCCGATACCCACCAACCATCGCCTCGACGAGGTGCAGTCCCGGCTCTTGTTGGCCGAGAGGaa                                                                                                           >  2:697822/1‑139 (MQ=255)

                                             tctTTGCCTGACACTTTGCTAAGCGCCACGGTATCGGAAACAAACACCACCGTCGTCGCCCGATACCCACCATCCATCGCCTCGACGAGGTGCAGTCCCGGCTCTTGTTGGCCGAGAGGAATATAAATGTTACCCGGCt                                                                                         <  2:254531/139‑1 (MQ=255)

                                              ctTTGCCTGACACTTTGCTAAGCGCCACGGTATCGGAAACAAACACCACCGTCGTCGCCCGATACCCACCAACCATCGCCTCGACGAGGTGCAGTCCCGGCTCTTGTTGGCCGAGAGGAATATAAATGTTACCCGGCTg                                                                                        >  2:461616/1‑139 (MQ=255)

                                              ctTTGCCTGACACTTTGCTAAGCGCCACGGTATCGGAAACAAACACCACCGTCGTCGCCCGATACCCACCAACCATCGCCTCGACGAGGTGCAGTCCCGGCTCTTGTTGGCCGAGAGGAATATAAATGTTACCCGGCTg                                                                                        >  2:1029047/1‑139 (MQ=255)

                                                 tGCCTGACACTTTGCTAAGCGCCACGGTATCGGAAACAAACACCACCGTCGTCGCCCGATACCCACCAACCATCGCCTCGACGAGGTGCAGTCCCGGCTCTTGTTGGCCGAGAGGAATATAAATGTTACCCGGCTgcgg                                                                                     <  1:697822/139‑1 (MQ=255)

                                                 tGCCTGACACTTTGCTAAGCGCCACGGTATCGGAAACAAACACCACCGTCGTCGCCCGATACCCACCAACCATCGCCTCGACGAGGTGCAGTCCCGGCTCTTGTTGGCCGAGAGGAATATAAATGTTACCCGGCTgcgg                                                                                     <  1:1029047/139‑1 (MQ=255)

                                                    cTGACACTTTGCTAAGCGCCACGGTATCGGAAACAAACACCACCGTCGTCGCCCGATACCCACCAACCATCGCCTCGACGAGGTGCAGTCCCGGCTCTTGTTGGCCGAGAGGAATATAAATGTTACCCGGCTGCGGCga                                                                                  >  1:133463/1‑139 (MQ=255)

                                                           tttGCTAAGCGCCACGGTATCGGAAACAAACACCACCGTCGTCGCCCGATACCCACCAACCATCGCCTCGACGAGGTGCAGTCCCGGCTCTTGTTGGCCgag                                                                                                                >  1:560222/1‑102 (MQ=255)

                                                           tttGCTAAGCGCCACGGTATCGGAAACAAACACCACCGTCGTCGCCCGATACCCACCAACCATCGCCTCGACGAGGTGCAGTCCCGGCTCTTGTTGGCCgag                                                                                                                <  2:560222/102‑1 (MQ=255)

                                                             tGCTAAGCGCCACGGTATCGGAAACAAACACCACCGTCGTCGCCCGATACCCACCAACCATCGCCTCGACGAGGTGCAGTCCCGGCTCTTGTTGGCCGagag                                                                                                              >  2:960285/1‑102 (MQ=255)

                                                             tGCTAAGCGCCACGGTATCGGAAACAAACACCACCGTCGTCGCCCGATACCCACCAACCATCGCCTCGACGAGGTGCAGTCCCGGCTCTTGTTGGCCGagag                                                                                                              <  1:960285/102‑1 (MQ=255)

                                                              gCTAAGCGCCACGGTATCGGAAACAAACACCACCGTCGTCGCCCGATACCCACCAACCATCGCCTCGACGAGGTGCAGTCCCGGCTCTTGTTGGCCGAGAGGAATATAAATGTTACCCGGCTGCGGCGAGATGAAATTg                                                                        <  2:888408/139‑1 (MQ=255)

                                                                       cACGGTATCGGAAACAAACACCACCGTCGTCGCCCGATACCCACCAACCATCGCCTCGACGAGGTGCAGTCCCGGCTCTTGTTGGCCgag                                                                                                                >  2:576535/1‑90 (MQ=255)

                                                                       cACGGTATCGGAAACAAACACCACCGTCGTCGCCCGATACCCACCAACCATCGCCTCGACGAGGTGCAGTCCCGGCTCTTGTTGGCCgag                                                                                                                <  1:576535/90‑1 (MQ=255)

                                                                       cACGGTATCGGAAACAAACACCACCGTCGTCGCCCGATACCCACCAACCATCGCCTCGACGAGGTGCAGTCCCGGCTCTTGTTGGCCGAGAGGAATATAAATGTTACCCGGCTGCGGCGAGATGAAATTGCTGGATgcg                                                               >  1:370444/1‑139 (MQ=255)

                                                                         cGGTATCGGAAACAAACACCACCGTCGTCGCCCGATACCCACCAACCATCGCCTCGACGAGGTGCAGTCCCGGCTCTTGTTGGCCGAGAGGAATATAAATGTTACCCGGCTGCGGCGAGATGAAATTGCTGGATGCGcc                                                             >  1:1018975/1‑139 (MQ=255)

                                                                            tATCGGAAACAAACACCACCGTCGTCGCCCGATACCCACCAACCAGCGCCTCGACGAGGTGCAGTCCCGGCTCTTGTTGGCCGAGAGGAATATAAATGTTACCCGGCTGCGGCGAGATGAAATTGCTGGATGCGCCTTc                                                          <  1:873393/139‑1 (MQ=255)

                                                                             aTCGGAAACAAACACCACCGTCTTCGCCCGATACACACCAAACATCGCCTCGACGAGGGGCAGTCCCGGCTCTTGTTGGCCGGGAGGAATATAAAGGTTACGCGGCTGCGGCGAGATGAAATTGCTGGATGCGCCTTcc                                                         <  2:626852/139‑1 (MQ=255)

                                                                             aTCGGAAACAAACACCACCGTCGTCGCCCGATACCCACCAACCATCGCCTCGACGAGGTGCAGTCCCGGCTCTTGTTGGCCGAGAGGAATATAAATGTTACCCGGCTGCGGCGAGATGAAATTGCTGGATGCGCCTTcc                                                         <  2:133463/139‑1 (MQ=255)

                                                                              tCGGAAACAAACACCACCGTCGTCGCCCGATACCCACCAACCATCGCCTCGACGAGGTGCAGTCCCGGCTCTTGTTGGCCGAGAGGAATATAAATGTTACCCGGCTGCGGCGAGATGAAATTGCTGGATGCGCCTTCCa                                                        >  1:554527/1‑139 (MQ=255)

                                                                                    acaaacaCCACCGTCGTCGCCCGATACCCACCAACCATCGCCTCGACGAGGTGCAGTCCCGGCTCTTGTTGGCCGAGAGGAATATAAATGTTACCCGGCTGCGGCGAGATGAAATTGCTGGATGCGCCTTCCAGTTTTa                                                  >  1:849290/1‑139 (MQ=255)

                                                                                      aaacaCCACCGTCGTCGCCCGATACCCACCAACCATCGCCTCGACGAGGTGCAGTCCCGGCTCTTGTTGGCCgag                                                                                                                >  1:456249/1‑75 (MQ=255)

                                                                                      aaacaCCACCGTCGTCGCCCGATACCCACCAACCATCGCCTCGACGAGGTGCAGTCCCGGCTCTTGTTGGCCgag                                                                                                                <  2:456249/75‑1 (MQ=255)

                                                                                               cgtcgtCGCCCGATACCCACCAACCATCGCCTCGACGAGGTGCAGTCCCGGCTCTTGTTGGCCGAGAGGAATATAAATGTTACCCGGCTGCGGCGAGATGAAATTGCTGGATGCGCCTTCCAGTTTTACCCCTtgctgc                                       <  1:513075/139‑1 (MQ=255)

                                                                                                gtcgtcGCCCGATACCCACCAACCATCGCCTCGACGAGGTGCAGTCCCGGCTCTTGTTGGCCGAGAGGAATATAAATGTTACCCGGCTGCGGCGAGATGAAATTGCTGGATGCGCCTTCCAGTTTTACCCCTTGCTGCg                                      >  2:780467/1‑139 (MQ=255)

                                                                                                   gtcgCCCGATAC‑‑‑CCAACCATCGCCTCGACGAGGTGCAGTCCCGGCTCTTGTTGGCCGAGAGGAATATAAATGTTACCCGGCTGCGGCGAGATGAAATTGCTGGATGCGCCTTCCAGTTTTACCCCTTGCTGCGGCTCGa                                <  1:71475/139‑1 (MQ=255)

                                                                                                      gCCCGATACCCACCAACCATCGCCTCGACGAGGTGCAGTCCCGGCTCTTGTTGGCCGAGAGGAATATAAATGTTACCCGGCTGCGGCGAGATGAAATTGCTGGATGCGCCTTCCAGTTTTACCCCTTGCTGCGGCTCGa                                <  2:370444/139‑1 (MQ=255)

                                                                                                      gCCCGATACCCACCAACCATCGCCTCGACGAGGTGCAGTCCCGGCTCTTGTTGGCCGAGAGGAATATAAATGTTACCCGGCTGCGGCGAGATGAAATTGCTGGATGCGCCTTCCAGTTTTACCCCTTGCTGCGGCTCGa                                <  2:554527/139‑1 (MQ=255)

                                                                                                          gATACCCACCAACCATCGCCTCGACGAGGTGCAGTCCCGGCTCTTGTTGGCCGAGAGGAATATAAATGTTACCCGGCTGCGGCGAGATGAAATTGCTGGATGCGCCTTCCAGTTTTACCCCTTGCTGCGGCTCGAACgg                            >  2:1079612/1‑139 (MQ=255)

                                                                                                              cccACCAACCATCGCCTCGACGAGGTGCAGTCCCGGCTCTTGTTGGCCGAGAGGAATATAAATGTTACCCGGCTGCGGCGAGATGAAATTGCTGGATGCGCCTTCCAGTTTTACCCCTTGCTGCGGCTCGAACGGTTTa                        <  1:780467/139‑1 (MQ=255)

                                                                                                                 accaaccaTCGCCTCGACGAGGTGCAGTCCCGGCTCTTGTTGGCCGAGAGGAATATAAATGTTACCCGGCTGCGGCgag                                                                                 <  2:237632/79‑1 (MQ=255)

                                                                                                                 accaaccaTCGCCTCGACGAGGTGCAGTCCCGGCTCTTGTTGGCCGAGAGGAATATAAATGTTACCCGGCTGCGGCgag                                                                                 >  1:237632/1‑79 (MQ=255)

                                                                                                                      ccaTCGCCTCGACGAGGTGCAGTCCCGGCTCTTGTTGGCCGAGAGGAATATAAATGTTACCCGGCTGCGGCGAGATGAAATTGCTGGATGCGCCTTCCAGTTTTACCCCTTGCTGCGGCTCGAACGGTTTAGCCTGCCa                <  1:1064574/139‑1 (MQ=255)

                                                                                                                         tCGCCTCGACGAGGTGCAGTCCCGGCTCTTGTTGGCCGAGAGGAATATAAATGTTACCCGGCTGCGGCGAGATGAAATTGCTGGATGCGCCTTCCAGTTTTACCCCTTGCTGCGGCTCGAACGGTTTAGCCTg                   <  1:645837/133‑1 (MQ=255)

                                                                                                                         tCGCCTCGACGAGGTGCAGTCCCGGCTCTTGTTGGCCGAGAGGAATATAAATGTTACCCGGCTGCGGCGAGATGAAATTGCTGGATGCGCCTTCCAGTTTTACCCCTTGCTGCGGCTCGAACGGTTTAGCCTg                   >  2:645837/1‑133 (MQ=255)

                                                                                                                                    aGGTGCAGTCCCGGCTCTTGTTGGCCGAGAGGAATATAAATGTTACCCGGCTGCGGCGAGATGAAATTGCTGGATGCGCCTTCCAGTTTTACCCCTTGCTGCGGCTCGAACGGTTTAGCCTGCCATAGTGGATAACGGa  <  1:951818/139‑1 (MQ=255)

                                                                                                                                    aGGTGCAGTCCCGGCTCTTGTTGGCCGAGAGGAATATAAATGTTACCCGGCTGCGGCGAAATGAAATTGCTGGATGCGCCTTCCAGTTTTACCCCTTGCTGCGGCTCGAACGGTTTAGCCTGCCATAGTGGATAACGGa  <  2:1018975/139‑1 (MQ=255)

GGCTTCGCTTCACCCTGTTTTTTACCCGCGGTCCACACCAGAAGCTCTTTGCCTGACACTTTGCTAAGCGCCACGGTATCGGAAACAAACACCACCGTCGTCGCCCGATACCCACCAACCATCGCCTCGACGAGGTACAGTCCCGGCTCTTGTTGGCCGAGAGGAATATAAATGTTACCCGGCTGCGGCGAGATGAAATTGCTGGATGCGCCTTCCAGTTTTACCCCTTGCTGCGGCTCGAACGGTTTAGCCTGCCATAGTGGATAACGGA  >  NC_000913/2333555‑2333825

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A