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
A17 F13 I0 R1	91	33.2	766976	92.9%	712520	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%	74.2 / NA	25	R7G (CGC→GGC)	USA300HOU_1679	sensor histidine kinase
Reads supporting (aligned to +/- strand): ref base G (0/0); new base C (16/9); total (16/9)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TAAATATATGATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATCA  >  CP000730/1797636‑1797901

taaatcTATGATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCcgtgg                                                                                                                               <  1:76612/141‑1 (MQ=255)

     ttattgtCTTGCATCTGTTGCTAGAGCTTGGTCGTGTATTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGaaa                                                                                                                          <  2:57783/135‑1 (MQ=255)

       atGATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACt                                                                                                                        >  1:186780/1‑141 (MQ=255)

            cTTGCATCTGTTTCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTtcatc                                                                                                                   <  2:376775/141‑1 (MQ=255)

               gCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCAtt                                                                                                                >  1:239011/1‑141 (MQ=255)

                cATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATCAAACATATGTGCTGGAAGCGTGAATAATAGTGCCTAAGGTAACAAAACTGATAATTAATCTACTGCTTTTCTATAACATTAAGCCGTGGTGAGACTTGATCAttt                                                                                                               >  1:343600/1‑140 (MQ=255)

                         cTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAATCTTAAGCCGTGGTGAAACTTCATCATTCTTCTTTAgg                                                                                                      >  2:262259/1‑141 (MQ=255)

                                    tCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAAtt                                                                                           >  1:147858/1‑141 (MQ=255)

                                     cGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTTTTTCCAAttt                                                                                          >  2:254302/1‑141 (MQ=255)

                                     cGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACAATAAGCCGGGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAAttt                                                                                          >  1:164438/1‑141 (MQ=255)

                                        gtTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTtata                                                                                       >  1:244803/1‑141 (MQ=255)

                                               tgttAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAg                                                                                <  1:20785/138‑1 (MQ=255)

                                                   aaaaCATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCAc                                                                            <  1:225387/141‑1 (MQ=255)

                                                     aaCATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGGTAAGTAATATACTGCTTATCAATAACATTAAGCCGTGGAGAAACTCCATCAGTGTTCTTCAGGCATTTCCAATTTATAGACTAAGcaagcc                                                                          >  2:11549/1‑136 (MQ=255)

                                                        atatGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTTTAGCCTAAGCCACGcaca                                                                       >  1:76343/1‑141 (MQ=255)

                                                         tatCTGAGGGAAGCGAGGACAATAAGGCCTAATGTAACATAACTGAAAAATAATTTGCTACGGATAATTTACATTTAGCCGGTTTTTAACTTCAGCATTGTTCTTTAGGTCTTTCCGATTTATAGCCTAAGCCACGCACAg                                                                      <  2:62743/141‑1 (MQ=255)

                                                                                               aaatCTGATAATTAATATGCTGCTTTGCAATAACATTAAGCCGTGGGTAAACTTCATCCTTGTTCTTTAGGTCTTTCTAATTTATAGCCTAAGCTACGCACAGTTTTAATAAGGTGTGGCTTCTTAGGATTATCTTCTAAt                                <  2:44139/141‑1 (MQ=255)

                                                                                               aaaaCTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAACCCACTCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAAt                                <  2:80938/141‑1 (MQ=255)

                                                                                                     gATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTAtct                          >  2:193952/1‑141 (MQ=255)

                                                                                                      aTAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTAtctc                         >  2:158200/1‑141 (MQ=255)

                                                                                                              tataCTGCTTATAAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTATGATTATGTTCTAATTTATCTTTTAAATGa                 >  2:172825/1‑141 (MQ=255)

                                                                                                                      ttATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATg         >  2:288448/1‑141 (MQ=255)

                                                                                                                       tATCAATAACATTAAGCCGTGGTGAAACTTCATCATCGTTCTTTAGGTCTTTCCTATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATATCTTAAATGACTGATATGt        <  1:213816/141‑1 (MQ=255)

                                                                                                                            aTAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTCCATc   >  2:380747/1‑141 (MQ=255)

                                                                                                                            aTAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATAACTGAAATGTACATc   >  2:215055/1‑141 (MQ=255)

                                                                                                                             tAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATca  <  2:186780/141‑1 (MQ=255)

TAAATATATGATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATCA  >  CP000730/1797636‑1797901

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