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
A7 F1 I1 R1	776	60.0	3074904	90.1%	2770488	104.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,769,648	(C)_6→5	intergenic (+162/‑55)	yfjQ → / → yfjR	CP4‑57 prophage, uncharacterized protein/CP4‑57 prophage, putative DNA‑binding transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,769,643	0	C	.	100.0%	174.8 / NA	42	intergenic (+157/‑60)	yfjQ/yfjR	CP4‑57 prophage, uncharacterized protein/CP4‑57 prophage, putative DNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand): ref base C (0/0); new base . (24/18); total (24/18)

TTAATATCGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGTCTGGTTGCGGGT  >  NC_000913/2769508‑2769777

ttAATATCGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGcccc                                                                                                                                     <  1:676838/139‑1 (MQ=255)

      tCGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCttt                                                                                                                              >  1:793021/1‑139 (MQ=255)

       cGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTa                                                                                                                             >  2:856451/1‑139 (MQ=255)

       cGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTa                                                                                                                             >  2:1257104/1‑139 (MQ=255)

       cGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTa                                                                                                                             >  1:95945/1‑139 (MQ=255)

         gACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAGTAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTaaa                                                                                                                           >  2:660316/1‑139 (MQ=255)

         gACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCttt                                                                                                                              <  1:1054463/136‑1 (MQ=255)

         gACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCttt                                                                                                                              >  2:1054463/1‑136 (MQ=255)

         gACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTaaa                                                                                                                           <  1:1257104/139‑1 (MQ=255)

         gACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTaaa                                                                                                                           <  1:856451/139‑1 (MQ=255)

                   gTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCAcat                                                                                                                 <  2:95945/139‑1 (MQ=255)

                   gTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCAcat                                                                                                                 <  1:138691/139‑1 (MQ=255)

                      cGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATcaca                                                                                                                  >  1:111871/1‑135 (MQ=255)

                      cGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATcaca                                                                                                                  <  2:111871/135‑1 (MQ=255)

                                   gCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGtt                                                                                                  >  2:16667/1‑138 (MQ=255)

                                   gCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGtt                                                                                                  <  1:16667/138‑1 (MQ=255)

                                       gtgtGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGcccc                                                                                                                                     <  2:79520/100‑1 (MQ=255)

                                       gtgtGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGcccc                                                                                                                                     >  1:79520/1‑100 (MQ=255)

                                        tgtgCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACttt                                                                                            <  2:1392057/139‑1 (MQ=255)

                                                  tCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGtt                                                                                                  >  1:536622/1‑123 (MQ=255)

                                                  tCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGtt                                                                                                  <  2:536622/123‑1 (MQ=255)

                                                       cGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAAtctct                                                                              <  2:743543/138‑1 (MQ=255)

                                                       cGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAAtctct                                                                              >  1:743543/1‑138 (MQ=255)

                                                                   ttAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTaa                                                                                                                            <  2:1322042/80‑1 (MQ=255)

                                                                   ttAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTaa                                                                                                                            >  1:1322042/1‑80 (MQ=255)

                                                                   ttAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTtca                                                                                                         <  2:751448/99‑1 (MQ=255)

                                                                   ttAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTtca                                                                                                         >  1:751448/1‑99 (MQ=255)

                                                                       cccccGTTACATCTGGCTTTTGCAGAAATAAAAAGTAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAAc                                                             <  1:660316/139‑1 (MQ=255)

                                                                          ccGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTg                                                                                        >  1:353175/1‑109 (MQ=255)

                                                                          ccGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTg                                                                                        <  2:353175/109‑1 (MQ=255)

                                                                                                            gTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCggct                                             >  1:444302/1‑118 (MQ=255)

                                                                                                            gTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCggct                                             <  2:444302/118‑1 (MQ=255)

                                                                                                             tttCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTc                                                                                           <  1:157781/71‑1 (MQ=255)

                                                                                                             tttCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTc                                                                                           >  2:157781/1‑71 (MQ=255)

                                                                                                               tCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAAt                     >  2:806173/1‑139 (MQ=255)

                                                                                                                             aCCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGTCTGGTTg       >  1:432200/1‑139 (MQ=255)

                                                                                                                                cTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGTCTGGTTGCgg    <  2:793021/139‑1 (MQ=255)

                                                                                                                                  gTCCG‑CCCCCTCTTTAAAGTAATCACATTATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGTCTGGTTGCGGGt  >  2:412325/1‑139 (MQ=255)

                                                                                                                                  gTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTggctgtca                                     >  1:1156707/1‑104 (MQ=255)

                                                                                                                                  gTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTggctgtca                                     <  2:1156707/104‑1 (MQ=255)

                                                                                                                                  gTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGTCTGGTTGCGGGt  >  1:921811/1‑139 (MQ=255)

                                                                                                                                  gTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGTCTGGTTGCGGGt  >  1:478558/1‑139 (MQ=255)

                                                                                                                                  gTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGTCTGGTTGCGGGt  >  2:683232/1‑139 (MQ=255)

                                                                                                                                  gTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGTCTGGTTGCGGGt  >  2:414664/1‑139 (MQ=255)

                                                                                                                                  gTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGTCTGGTTGCGGGt  >  2:379986/1‑139 (MQ=255)

TTAATATCGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGTCTGGTTGCGGGT  >  NC_000913/2769508‑2769777

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 31 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A