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 I1 R1	759	65.2	3386260	90.7%	3071337	101.6

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%	113.4 / NA	36	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 (16/20); total (16/20)

GTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACGCCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAACTCAGCAAAACCTGATCGATGGT  >  NC_000913/3187460‑3187720

gTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCAcc                                                                                                                            <  2:1690266/139‑1 (MQ=255)

           caaAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCaa                                                                                                                 <  1:1403129/139‑1 (MQ=255)

                                    cGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACAAAACTg                                                                                        >  2:1022566/1‑139 (MQ=255)

                                    cGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGAAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACTAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTg                                                                                        <  2:1124419/139‑1 (MQ=255)

                                     gTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATcc                                                                                                                               >  2:156492/1‑99 (MQ=255)

                                     gTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATcc                                                                                                                               >  2:1207414/1‑99 (MQ=255)

                                     gTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATcc                                                                                                                               <  1:156492/99‑1 (MQ=255)

                                     gTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATcc                                                                                                                               <  1:1207414/99‑1 (MQ=255)

                                                     ttCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCa                                                                       <  1:1022566/139‑1 (MQ=255)

                                                     ttCCCAATTTGAAACTGATGGCCAATTACCCGTCGGC‑AATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCag                                                                      <  2:1385254/139‑1 (MQ=255)

                                                       cccAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGAc                                                                                                                       <  1:1061050/89‑1 (MQ=255)

                                                       cccAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGAc                                                                                                                       >  2:1061050/1‑89 (MQ=255)

                                                                  aCTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCaga                                                                     <  2:749205/128‑1 (MQ=255)

                                                                  aCTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCaga                                                                     >  1:749205/1‑128 (MQ=255)

                                                                              ttACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTa                                              >  2:97879/1‑139 (MQ=255)

                                                                                               ttCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGaa                             >  2:945243/1‑139 (MQ=255)

                                                                                                tCACTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGaaa                            >  1:707735/1‑139 (MQ=255)

                                                                                                  aCTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGAcc                                                                                                                      >  2:1059431/1‑47 (MQ=255)

                                                                                                  aCTAAGCACTCTGATTAATAATAAGAGGACACCAATCCACCTTGAcc                                                                                                                      <  1:1059431/47‑1 (MQ=255)

                                                                                                            ctGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGaaa                            <  1:1298772/127‑1 (MQ=255)

                                                                                                            ctGATTAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGaaa                            >  2:1298772/1‑127 (MQ=255)

                                                                                                                ttAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGacac                                                                         >  2:423009/1‑78 (MQ=255)

                                                                                                                ttAATAATAAGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGacac                                                                         <  1:423009/78‑1 (MQ=255)

                                                                                                                      ataaGAGGACACCAATCCACCTTGTCCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAACTCAGCAAAACCTGATCGa      <  1:945243/139‑1 (MQ=255)

                                                                                                                      ataaGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAACTCAGCAAAACCTGATCGa      <  1:97879/139‑1 (MQ=255)

                                                                                                                       taaGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCg                                                                               <  1:344326/65‑1 (MQ=255)

                                                                                                                       taaGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCg                                                                               >  2:344326/1‑65 (MQ=255)

                                                                                                                       taaGAGGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAACTCAGCAAAACCTGATCGAt     <  2:707735/139‑1 (MQ=255)

                                                                                                                         agagGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGtt                                                                                   <  2:677623/59‑1 (MQ=255)

                                                                                                                         agagGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGtt                                                                                   >  1:677623/1‑59 (MQ=255)

                                                                                                                         agagGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGt                                                                              >  1:423345/1‑64 (MQ=255)

                                                                                                                         agagGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGt                                                                              <  2:423345/64‑1 (MQ=255)

                                                                                                                         agagGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAACTCAGCAAAACCTGATCGATgg   >  1:499038/1‑139 (MQ=255)

                                                                                                                          gagGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAACTCAGCAAAACCTGATCGATGgt  <  2:499038/139‑1 (MQ=255)

                                                                                                                           agGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGtt                                                                                   <  2:304407/57‑1 (MQ=255)

                                                                                                                           agGACACCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGtt                                                                                   >  1:304407/1‑57 (MQ=255)

GTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCCGTCGGCAAATATTCACTAAGCACTCTGATTAATAATAAGAGGACGCCAATCCACCTTGACCTCCAATGGGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAACTCAGCAAAACCTGATCGATGGT  >  NC_000913/3187460‑3187720

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