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
A2 F1 I2 R1	764	42.0	2018750	95.5%	1927906	109.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,034,536	G→A	pseudogene (486/663 nt)	yedS →	pseudogene, outer membrane protein homology, putative outer membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,034,536	0	G	A	100.0%	129.6 / NA	41	pseudogene (486/663 nt)	yedS	pseudogene, outer membrane protein homology, putative outer membrane protein
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (22/19); total (22/19)

TCGTATATGACGTAGAAGCATGGACCGATATGCTGCCAGAATTTGGTGGCGATACCTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAGGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTAGTGGTGATGGCCGTAGCCTTTCCAAAGAAAATGGTGATGGTTTCGGTATG  >  NC_000913/2034403‑2034665

tCGTATATGACGTAGAAGCATGGACCGATATGCTGCCAGAATTTGGTGGCGATACCTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGa                                                                                                                              >  2:775308/1‑139 (MQ=255)

 cGTATATGACGTAGAAGCATGGACCGATATGCTGCCAGAATTTGGTGGCGATACCTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGAt                                                                                                                             <  1:775308/139‑1 (MQ=255)

        gACGTAGAAGCATGGACCGATATGCTGCCAGAATTTGGTGGCGATACCTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGa                                                                                                                      >  2:324695/1‑139 (MQ=255)

          cGTAGAAGCATGGACCGATATGCTGCCAGAATTTGGTGGCGATACCTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACACTGGCTTCTTTGGTTAAGTCGATGGCTTGAAc                                                                                                                    >  2:304686/1‑139 (MQ=255)

          cGTAGAAGCATGGACCGATATGCTGCCAGAATTTGGTGGCGATACCTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGc                                                                                                                          >  1:1002050/1‑133 (MQ=255)

          cGTAGAAGCATGGACCGATATGCTGCCAGAATTTGGTGGCGATACCTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGc                                                                                                                          <  2:1002050/133‑1 (MQ=255)

          cGTAGAAGCATGGACCGATATGCTGCCAGAATTTGGTGGCGATACCTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAAc                                                                                                                    >  1:374756/1‑139 (MQ=255)

            tAGAAGCATGGACCGATATGCTGCCAGAATTTGGTGGCGATACCTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAActt                                                                                                                  >  1:306962/1‑139 (MQ=255)

            tAGAAGCATGGACCGATATGCTGCCAGAATTTGGTGGCGATACCTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAActt                                                                                                                  >  2:104113/1‑139 (MQ=255)

             aGAAGCATGGACCGATATGCTGCCAGAATTTGGTGGCGATACCTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGaa                                                                                                                     <  2:496910/135‑1 (MQ=255)

             aGAAGCATGGACCGATATGCTGCCAGAATTTGGTGGCGATACCTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGaa                                                                                                                     >  1:496910/1‑135 (MQ=255)

                   aTGGACCGATATGCTGCCAGAATTTGGTGGCGATACCTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAActttgctttg                                                                                                           <  2:306962/139‑1 (MQ=255)

                         cGATATGCTGCCAGAATTTGGTGGCGATACCTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAatat                                                                                                     <  2:374756/139‑1 (MQ=255)

                                            ggtggCGATACCTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAgtg                                                                                  >  2:311836/1‑139 (MQ=255)

                                                               gcgcTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGa                                                               >  2:216113/1‑139 (MQ=255)

                                                                cgcTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGaa                                                              <  1:104113/139‑1 (MQ=255)

                                                                cgcTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGaa                                                              <  1:311836/139‑1 (MQ=255)

                                                                cgcTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGaa                                                              <  1:371108/139‑1 (MQ=255)

                                                                    gACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTCTGCAATATCAGGGTAATAATGa                                                                                       >  2:598470/1‑110 (MQ=255)

                                                                    gACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTCTGCAATATCAGGGTAATAATGa                                                                                       <  1:598470/110‑1 (MQ=255)

                                                                     aCAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTc                                                         <  1:924075/139‑1 (MQ=255)

                                                                          ttCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTa                                                    <  1:324695/139‑1 (MQ=255)

                                                                               gAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTAgtggt                                               >  2:732642/1‑139 (MQ=255)

                                                                                               ggTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTAGTGGTGATGGCCGTAGCCttt                               >  2:912302/1‑139 (MQ=255)

                                                                                               ggTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATGCGGGCAGGAAGGTTCCGGTAGTGGTGATGGCCGTAGCCttt                               >  2:727858/1‑139 (MQ=255)

                                                                                                   ttGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAActttgc                                                                                                               >  1:515249/1‑55 (MQ=255)

                                                                                                   ttGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAActttgc                                                                                                               <  2:515249/55‑1 (MQ=255)

                                                                                                    tGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCg                                                                                                                               >  1:436877/1‑38 (MQ=255)

                                                                                                    tGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCg                                                                                                                               <  2:436877/38‑1 (MQ=255)

                                                                                                     gCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGa                                                               >  1:6017/1‑101 (MQ=255)

                                                                                                     gCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGa                                                               <  2:6017/101‑1 (MQ=255)

                                                                                                          cTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGa                                                                                       >  1:161884/1‑72 (MQ=255)

                                                                                                          cTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGa                                                                                       <  2:161884/72‑1 (MQ=255)

                                                                                                           tACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAActttgc                                                                                                               >  1:247536/1‑47 (MQ=255)

                                                                                                           tACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAActttgc                                                                                                               <  2:247536/47‑1 (MQ=255)

                                                                                                           tACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTAGTGGTGa                                             >  2:329700/1‑113 (MQ=255)

                                                                                                           tACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTAGTGGTGa                                             <  1:329700/113‑1 (MQ=255)

                                                                                                                      tGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTcc                                                        >  1:888904/1‑91 (MQ=255)

                                                                                                                      tGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTcc                                                        <  2:888904/91‑1 (MQ=255)

                                                                                                                          ttcttTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTAGTGGTGATGGCCGTAGCCTTTCCAAAGAAAATGGTGATGGTTTCGGTa    <  1:732642/139‑1 (MQ=255)

                                                                                                                            cttTGGTGAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCACGAAGGTTCCGGTAGTGGTGATGGCCGTAGCCTTTCCAAAGAAATTGGTGATGGTTTCGGTATg  >  1:661824/1‑139 (MQ=255)

TCGTATATGACGTAGAAGCATGGACCGATATGCTGCCAGAATTTGGTGGCGATACCTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAGGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTAGTGGTGATGGCCGTAGCCTTTCCAAAGAAAATGGTGATGGTTTCGGTATG  >  NC_000913/2034403‑2034665

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `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