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 F57 I0 R1	30	26.7	570066	96.5%	550113	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%	87.3 / NA	26	R7G (CGC→GGC)	USA300HOU_1679	sensor histidine kinase
Reads supporting (aligned to +/- strand): ref base G (0/0); new base C (14/12); total (14/12)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

AATATATGATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATCAACAATTC  >  CP000730/1797638‑1797908

aataTATGATCTTGCATCTGTTGCTAGGTCCTGTTCCTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCgtggtg                                                                                                                                    <  1:162742/141‑1 (MQ=255)

             gCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTAATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCAtt                                                                                                                       >  1:68666/1‑141 (MQ=255)

              cATCTGTTGCTAGAGCTTGTTCGTGCTCAGCGGGTAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTg                                                                                                                      >  1:67645/1‑141 (MQ=255)

                tCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAGTAATGCCTAATGTAACAAAACTGAGAATTAATATACTGCTTATCAATAACATTAAGCCGGGGGGAAACGTCATCATTGtt                                                                                                                    >  1:166871/1‑141 (MQ=255)

                         agagCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTc                                                                                                           >  2:128042/1‑141 (MQ=255)

                          gagCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAgatat                                                                                                          >  2:210816/1‑137 (MQ=255)

                              ttGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTcc                                                                                                      <  2:149175/141‑1 (MQ=255)

                                             tGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAg                                                                                       >  2:139000/1‑141 (MQ=255)

                                                             atttaaGCGTTAATAATAATGCCTAATGTAACAAAACTAATAATTAATATACTGCTTATCAATAACATTAAGCCTTAGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTtaa                                                                       <  2:155341/137‑1 (MQ=255)

                                                                 aaGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAg                                                                   >  1:197182/1‑141 (MQ=255)

                                                                   gCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGtt                                                                 >  1:195527/1‑141 (MQ=255)

                                                                     gTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGTTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTtgt                                                               <  2:207963/141‑1 (MQ=255)

                                                                       gaagaaTAATGCCGAATGTAACAAAACTGATAATTAATTGACTGCTTATCAATAACATTAAGTCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCATTTTTTTGGTTTTGCCCCGCACAGTTTTAATAAGTTGTgg                                                             <  2:32559/141‑1 (MQ=255)

                                                                            ataatGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGcttct                                                        <  1:139000/141‑1 (MQ=255)

                                                                                 gCCTAAGGTAAAAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGa                                                   <  2:29124/141‑1 (MQ=255)

                                                                                    tAATGTAACAGAACTGATCATTCATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGTTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTa                                                <  1:64300/141‑1 (MQ=255)

                                                                                       tctAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTAtct                                             <  1:213563/139‑1 (MQ=255)

                                                                                                        ttaatATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTaa                            <  1:257639/141‑1 (MQ=255)

                                                                                                                cTGCTTATCAATAACATTAACCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTAGCTCTTAAATGACTGa                    <  1:210023/141‑1 (MQ=255)

                                                                                                                       tCAATAACATTAAGCCGTGGTAAAACTGCATCATTATTCATTAGGTCTCTCCAATTTATAGCCTAAGCCACGCACAGGTTTAATAAGTCGTAGCTTCTCACGATTTTCTTCTTACTTATCGCCAAACTGACTGATATTTAc             >  2:146532/1‑141 (MQ=255)

                                                                                                                         aaTAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACAt           >  1:221099/1‑141 (MQ=255)

                                                                                                                          aTAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATc          <  2:68666/141‑1 (MQ=255)

                                                                                                                           tAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGCCTGATATGTACATca         >  2:26262/1‑141 (MQ=255)

                                                                                                                               aTTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATcaacaa     >  1:251041/1‑141 (MQ=255)

                                                                                                                                  aaGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATATATAGCCTAAGCCACGCACCGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTGTCTCTTAGATGACTGATAGGTACATCAACAAttt  >  1:172311/1‑140 (MQ=255)

                                                                                                                                  aaGCCGTGGTGAAACTTCATCATTGTTCTTAAGGTCTTTCCAATTTATAGCCTAAGCAACACACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATACGTACATCAACAAtcc  >  1:251436/1‑139 (MQ=255)

AATATATGATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATCAACAATTC  >  CP000730/1797638‑1797908

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