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
A10 F1 I2 R1	757	38.1	1607544	96.5%	1551279	117.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,187,588	G→A	pseudogene (162/2439 nt)	yqiG →	pseudogene, fimbrial export usher family,putative membrane, Not classified, putative membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,187,588	0	G	A	100.0%	97.9 / NA	32	pseudogene (162/2439 nt)	yqiG	pseudogene, fimbrial export usher family,putative membrane, Not classified, putative membrane protein
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (13/19); total (13/19)

GCCGTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACGCCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAACTCAGCAAAACCTGATCGATGG  >  NC_000913/3187457‑3187719

gCCGTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATcc                                                                                                                              <  1:449018/139‑1 (MQ=255)

             acaaAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCa                                                                                                                 <  2:180616/139‑1 (MQ=255)

              caaAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCTTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGATCTCCaa                                                                                                                <  1:230418/139‑1 (MQ=255)

              caaAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCaa                                                                                                                <  1:48058/139‑1 (MQ=255)

                aaGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATg                                                                                                              <  1:549367/139‑1 (MQ=255)

                            aaGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGa                                                                                                  <  1:267810/139‑1 (MQ=255)

                                                gTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCg                                                                              <  1:598983/139‑1 (MQ=255)

                                                 ttAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGt                                                                             <  2:225979/139‑1 (MQ=255)

                                                 ttAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGt                                                                             <  2:135735/139‑1 (MQ=255)

                                                          cccAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATACCCAAACTCCAGTTTCCGTGACACCaga                                                                    >  1:323264/1‑139 (MQ=255)

                                                          cccAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGt                                                                                   <  2:397051/124‑1 (MQ=255)

                                                          cccAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACAAAACTGCAGt                                                                                   >  1:397051/1‑124 (MQ=255)

                                                                         aTGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATACACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACattatt                                                     >  2:97722/1‑139 (MQ=255)

                                                                         aTGGCCAATTACCCGTCGGCAAATATACACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACattatt                                                     >  1:354776/1‑139 (MQ=255)

                                                                                         cGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAAt                                                                                                               <  2:427317/65‑1 (MQ=255)

                                                                                         cGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAAt                                                                                                               >  1:294843/1‑65 (MQ=255)

                                                                                         cGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAAt                                                                                                               >  1:427317/1‑65 (MQ=255)

                                                                                         cGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAAt                                                                                                               <  2:294843/65‑1 (MQ=255)

                                                                                         cGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGaa                                     <  2:354776/139‑1 (MQ=255)

                                                                                          ggCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAAt                                    >  2:632258/1‑139 (MQ=255)

                                                                                                         aGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACGTTATTAGGATTTACTGATGAATTTATTGAAAAAACTc                     >  1:662568/1‑139 (MQ=255)

                                                                                                              tctGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGacac                                                                        <  1:754064/83‑1 (MQ=255)

                                                                                                              tctGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGacac                                                                        >  2:754064/1‑83 (MQ=255)

                                                                                                                       taataaGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGAtt                                               >  1:636445/1‑99 (MQ=255)

                                                                                                                       taataaGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGAtt                                               <  2:636445/99‑1 (MQ=255)

                                                                                                                          taaGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAACTCAGCAAAACCTGATCGAt    <  2:242409/139‑1 (MQ=255)

                                                                                                                          taaGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAACTCAGCAAAACCTGATCGAt    <  1:97722/139‑1 (MQ=255)

                                                                                                                            agagGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAAc                                                           >  2:208611/1‑82 (MQ=255)

                                                                                                                            agagGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAAc                                                           <  1:208611/82‑1 (MQ=255)

                                                                                                                            agagGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAACTCAGCAAAACCTGATCGATgg  >  2:424421/1‑139 (MQ=255)

                                                                                                                            agagGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAACTCAGCAAAACCTGATCGATgg  >  2:602712/1‑139 (MQ=255)

                                                                                                                                gACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACt                                           <  1:637541/94‑1 (MQ=255)

GCCGTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACGCCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAACTCAGCAAAACCTGATCGATGG  >  NC_000913/3187457‑3187719

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A