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
A3 F1 I2 R1	58	36.1	1832140	90.7%	1661750	105.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,335,018	G→A	L543L (CTG→TTG)	yfaA ←	DUF2138 family protein, putative host defense protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,335,018	0	G	A	100.0%	109.4 / NA	32	L543L (CTG→TTG)	yfaA	DUF2138 family protein, putative host defense protein
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (19/13); total (19/13)

TCGACATTCAGCATTTCGCTATGGGCAACAACACAACACAGCCAGCAAATCAGCGCCAGCAGCCCGTGCCTCATAGCGGCTGCCAGGTTATGGGTAGCCACTGCCAGGCGGCACCGGGTTCCATCTGGGCCAGCTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCGGCATTAATAAAGTTTGTGCGGCGTTATAAAAAACCGGTTCGAGATTCTTCGGCAGACTGGTCAACGTTTCGTTACGCAGCAGTTTCGCTA  >  NC_000913/2334886‑2335152

tCGACATTCAGCATTTCGCTATGGGCAACAACACAACACAGCCAGCAAATCAGCGCCAGCAGCCCGTGCCTCATAGCGGCTGCCAGGTTATGGGTAGCCACTGCCAGGCGGCACCGGGTTCCATCTGGGCCAACTTCAt                                                                                                                                  >  1:672075/1‑139 (MQ=255)

  gACATTCAGCATTTCGCTATGGGCAACAACACAACACAGCCAGCAAATCAGCGCCAGCAGCCCGTGCCTCATAGCGGCTGCCAGGTTATGGGTAGCCACTGCCAGGCGGCACCGGGTTCCATCTGGGCCAACTTCATGa                                                                                                                                <  2:232850/139‑1 (MQ=255)

                cGCTATGGGCAACAACACAACACAGCCAGCAAATCAGCGCCAGCAGCCCGTGCCTCATAGCGGCTGCCAGGTTATGGGTAGCCACTGCCAGGCGGCACCGGGTTCCATCTGGGCCAACTTCATGACATAACGCGgttgt                                                                                                                  >  2:332659/1‑139 (MQ=255)

                                   acacaGCCAGCAAATCAGCGCCAGCAGCCCGTGCCTCATAGCGGCTGCCAGGTTATGGGTAGCCACTGCCAGGTGGCACCGGGTTCCATCTGGGCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCt                                                                                               <  2:767304/139‑1 (MQ=255)

                                       agccagcAAATCAGCGCCAGCAGCCCGTGCCTCATAGCGGCTGCCAGGTTATGGGTAGCCACTGCCAGGCGGCACCGGGTTCCATCTGGGCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCgg                                                                                           >  2:858363/1‑139 (MQ=255)

                                         ccagcAAATCAGCGCCAGCAGCCCGTGCCTCATAGCGGCTGCCAGGTTATGGGTAGCCACTGCCAGGCGGCACCGGGTTCCATCTGGGCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCGGCa                                                                                         <  1:388429/139‑1 (MQ=255)

                                         ccagcAAATCAGCGCCAGCAGCCCGTGCCTCATAGCGGCTGCCAGGTTATGGGTAGCCACTGCCAGGCGGCACCGGGTTCCATCTGGGCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCGGCa                                                                                         >  2:22301/1‑139 (MQ=255)

                                            gcAAATCAGCGCCAGCAGCCCGTGCCTCATAGCGGCTGCCAGGTTATGGGTAGCCACTGCCAGGCGGCACCGGGTTCCATCTGGGCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCGGCACta                                                                                      >  1:427128/1‑139 (MQ=255)

                                                        cagcagCCCGTGCCTCATAGCGGCTGCCAGGTTATGGGTAGCCACTGCCAGGCGGCACCGGGTTCCATCTGGGCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCGGCATTAATAAAGTTtgtg                                                                          <  1:858363/139‑1 (MQ=255)

                                                                              gCTGCCAGGTTATGGGTAGCCACTGCCAGGCGGCACCGGGTTCCATCTGGGCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCgg                                                                                           <  1:635030/100‑1 (MQ=255)

                                                                              gCTGCCAGGTTATGGGTAGCCACTGCCAGGCGGCACCGGGTTCCATCTGGGCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCgg                                                                                           >  2:635030/1‑100 (MQ=255)

                                                                              gCTGCCAGGTTATGGGTAGCCACTGCCAGGCGGCACCGGGTTCCATCTGGGCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCGGCATTAATAAAGTTTGTGCGGCGTTATAAAAAAcc                                                         <  1:493797/134‑1 (MQ=255)

                                                                              gCTGCCAGGTTATGGGTAGCCACTGCCAGGCGGCACCGGGTTCCATCTGGGCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCGGCATTAATAAAGTTTGTGCGGCGTTATAAAAAAcc                                                         >  2:493797/1‑134 (MQ=255)

                                                                                                gCCACTGCCGGGCGGCACCGGGTTCCATCTGGGCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCGGCATTAATAAAGTTTGTGCGGCGTTATAAAAAACCGGTTCGAGATTCTTCGGCAGACt                                  >  2:182639/1‑139 (MQ=255)

                                                                                                gCCACTGCCAGGCGGCACCGGGTTCCATCTGGGCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCGGCATTAATAAAGTTTGTGCGGCGTTCTAAAAAACCGGTTCGAGATTCCTCGGCAGACt                                  >  1:738375/1‑139 (MQ=255)

                                                                                                gCCACTGCCAGGCGGCACCGGGTTCCATCTGGGCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCGGCATAAATAAAGTTTGTGCGGCGTTATAAAAAACCGGTTCGAGATTCTTCGGCAGACt                                  >  2:55157/1‑139 (MQ=255)

                                                                                                 ccACTGCCAGGCGGCACCGGGTTCCATCTGGGCCAACTTCATGACATAACGCGGTTGTTGAGATAAGGCGTCCAGCTTCGGCATTAATAAAGTTTGTGCGGCGTTATAAAAAACCGGTTCGAGATTCTTCGGCAGACTg                                 >  2:410763/1‑139 (MQ=255)

                                                                                                   aCTGCCGGGCGGCACCGGGTTCCATCTGGGCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCGGCATTAATAAAGTTTGTGCGGCGTTATAAAAAACCGGTTCGAGATTCTTCGGCAGACTGGt                               <  1:182639/139‑1 (MQ=255)

                                                                                                       ccAGGCGGCACCGGGTTCCATCTGGGCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCGGCATTAATAAAGTTTGTGCGGCGTTATAAAAAACCGGTTCGAGATTCTTCGGCAGACTGGTCAAc                           >  1:104881/1‑139 (MQ=255)

                                                                                                               cACCGGGTTCCATCTGGGCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCGGCATTAATAAAGTTTGTGCGGCGTTATAAAAAACCGGTTCgaga                                                <  1:906762/110‑1 (MQ=255)

                                                                                                               cACCGGGTTCCATCTGGGCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCGGCATTAATAAAGTTTGTGCGGCGTTATAAAAAACCGGTTCgaga                                                >  2:906762/1‑110 (MQ=255)

                                                                                                               cACCGGGTTCCATCTGGGCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCGGCATTAATAAAGTTTGTGCGGCGTTATAAAAAACCGGTTCGAGATTCTTCGGCAGACTGGTCAACGTTTCGtt                   >  1:853921/1‑139 (MQ=255)

                                                                                                               cACCGGGTTCCATCTGGGCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCGGCATTAATAAAGTTTGTGCGGCGTTATAAAAAACCGGTTCGAGATTCTTCGGCAGACTGGTCAACGTTTCGtt                   >  2:850010/1‑139 (MQ=255)

                                                                                                                 ccGGGTTCCATCTGGGCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCt                                                                                               <  1:657994/61‑1 (MQ=255)

                                                                                                                 ccGGGTTCCATCTGGGCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCt                                                                                               >  2:657994/1‑61 (MQ=255)

                                                                                                                     gTTCCATCTGGGCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCGGCATTAATAAAGTTTGTGCGGCGTTATAAAAAACCGGTTCGAGATTCTTCGGCAGACTGGTCAACGTTTCGTTACgcag             <  2:427128/139‑1 (MQ=255)

                                                                                                                         cATCTGGGCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCGGCATTAATAAAGTTTGTGCGGCGTTATAAAAAACCGGTTCGAGATTCTTCGGCAGACTGGTCAACGTTTCGTTACGCAGCAGt         >  1:820932/1‑139 (MQ=255)

                                                                                                                           tCTGGGCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCGGCATTAATAAAGTTTGTGCGGCGTTATAAAAAACCGGTTCGAGATTCTTCGGCAGACTGGTCAACGTTTCGTTACGCAGCAGttt       >  2:316845/1‑139 (MQ=255)

                                                                                                                               ggCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCGGCATtaa                                                                                     >  1:732677/1‑57 (MQ=255)

                                                                                                                               ggCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCGGCATtaa                                                                                     <  2:732677/57‑1 (MQ=255)

                                                                                                                               ggCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCGGCATTAATAAAGTTTGTGCGGCGTTATAAAAAACCGGTTCGAGATTCTTCGGCAGACTGGTCAACGTTTCGTTACGCAGCAGTTTCGCt   <  1:316845/139‑1 (MQ=255)

                                                                                                                                gCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCGGCATTAATAAAGTTTGTGCGGCGTTATAAAAAACCGGTTCGAGATTCTTCGGCAGACTGGTCAACGTTTCGTTACGCAGCAGTTTCGCTa  <  1:332659/139‑1 (MQ=255)

TCGACATTCAGCATTTCGCTATGGGCAACAACACAACACAGCCAGCAAATCAGCGCCAGCAGCCCGTGCCTCATAGCGGCTGCCAGGTTATGGGTAGCCACTGCCAGGCGGCACCGGGTTCCATCTGGGCCAGCTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCGGCATTAATAAAGTTTGTGCGGCGTTATAAAAAACCGGTTCGAGATTCTTCGGCAGACTGGTCAACGTTTCGTTACGCAGCAGTTTCGCTA  >  NC_000913/2334886‑2335152

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