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
A13 F121 I0 R1	43	32.8	695000	96.9%	673455	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	1,797,772	G→C	100%	R7G (CGC→GGC)	USA300HOU_1679 ←	sensor histidine kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,797,772	0	G	C	100.0%	99.1 / NA	30	R7G (CGC→GGC)	USA300HOU_1679	sensor histidine kinase
Reads supporting (aligned to +/- strand): ref base G (0/0); new base C (16/14); total (16/14)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TGATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATCAACAAT  >  CP000730/1797644‑1797906

tGATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACtt                                                                                                                            >  1:24103/1‑141 (MQ=255)

 gATCTTGCATCTGTTGCTCGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATGCTGCTTGTAAATAACATTCGGCCTTGGTGGAGCTtc                                                                                                                           >  1:74601/1‑141 (MQ=255)

   tCTTGCATCTGTTTCTATACACTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAAAAACATTAAGCCGTGGTGAAACTtcat                                                                                                                         <  1:174541/141‑1 (MQ=255)

       gCATCTTTTGCTAGAGCTTGTTAGTGTTTTTCTGATAAATCATATGCGGTGGAAGCGTGATTAAGAATGCCTAATGTAACAAAACTAGTCGTTGATATATTTCTTATCAATAACATTAAGGCGTGGTGAACTTTCAGCAtt                                                                                                                     >  2:134009/1‑141 (MQ=255)

         aTCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGt                                                                                                                   <  2:64140/141‑1 (MQ=255)

             gTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCtt                                                                                                               <  2:327427/141‑1 (MQ=255)

                      gCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCttt                                                                                                      <  1:271622/141‑1 (MQ=255)

                       cTTGTTCGTGTTTTTCTGATAAAACATCTGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTc                                                                                                     <  2:70979/141‑1 (MQ=255)

                       cTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTc                                                                                                     >  1:174726/1‑141 (MQ=255)

                                               cATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCAACGcac                                                                             >  1:5701/1‑141 (MQ=255)

                                                 tatGTGATGGAAGCCTAAATAATAAGGCTCAATGTAACAAAACTGATAATTAATATACTTCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAg                                                                           <  2:42360/141‑1 (MQ=255)

                                                  atGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGt                                                                          >  1:75495/1‑141 (MQ=255)

                                                     tgATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGtttt                                                                       >  1:13672/1‑141 (MQ=255)

                                                             gCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGtt                                                               >  1:102325/1‑141 (MQ=255)

                                                              cGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTtg                                                              <  1:7322/141‑1 (MQ=255)

                                                                tGAAAAATAATGCCTAATGTAACAAAACTGCTAATTAATATAGTGCTTAACAAGAACAATAAGCCGAGGTGAAACTTCATCATTGTTCTTTCGGTCTTTCCAATTTATAGCCTAAGGCACGCCCAGTTTTAATAAGTtgtt                                                            >  2:209526/1‑140 (MQ=255)

                                                                         atGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCAGAGTTTTAATAAGTTGTGGCTTCTTAg                                                   <  2:214440/141‑1 (MQ=255)

                                                                         atGCCAAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCAGAGTTTTAATAAGTTGTGGCTTCTTAg                                                   <  2:214493/141‑1 (MQ=255)

                                                                                         aaCTAATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCCATTTATAGCCTAAGCCACGCACACTTTTAATAAGTTGTGGCTTCTTAGGTTTTTCTTCTAAttt                                   >  1:243978/1‑141 (MQ=255)

                                                                                                aattaatATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCtt                            >  1:217531/1‑141 (MQ=255)

                                                                                                  ttaatATACTGCTTATCAATAACATGAAGCCGTGGGGACACTTCATCATTGTTCTTTAGGTCTTTCCAATTGATAGCCTCAGCCACGCACAGTTTTAATAAGTTGTGGCTTCGTATGATTATCTTCTAATTTATCTCTCaa                          <  2:151882/141‑1 (MQ=255)

                                                                                                              ttATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATg              <  2:5701/141‑1 (MQ=255)

                                                                                                              ttATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATg              <  1:156416/141‑1 (MQ=255)

                                                                                                              ttATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATg              <  2:325033/141‑1 (MQ=255)

                                                                                                                  cAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACa          >  1:71758/1‑141 (MQ=255)

                                                                                                                    aTAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTACTTTATCTCTTAAATGACTGATATGTACATc        >  2:108054/1‑141 (MQ=255)

                                                                                                                    aTAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGGTATGTACATc        >  1:30409/1‑141 (MQ=255)

                                                                                                                    aTAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATc        >  2:108050/1‑141 (MQ=255)

                                                                                                                       aCATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATcaac     <  2:174726/141‑1 (MQ=255)

                                                                                                                          ttAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATCAACAAt  >  2:59557/1‑141 (MQ=255)

TGATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATCAACAAT  >  CP000730/1797644‑1797906

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A