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 F123 I0 R1	46	52.8	1143652	95.1%	1087613	141.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	2,027,672	C→A	100%	G92V (GGC→GTC)	vraS ←	sensor histidine kinase VraS

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,027,672	0	C	A	97.4%	105.4 / ‑5.1	35	G92V (GGC→GTC)	vraS	sensor histidine kinase VraS
Reads supporting (aligned to +/- strand): ref base C (1/0); new base A (20/14); total (21/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.59e-01
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

ATTAATATTATAATTTTCATTGGTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGG  >  CP000730/2027539‑2027808

atTAATATTATAATTTTCATTGGTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACAGt                                                                                                                                   >  2:396676/1‑141 (MQ=255)

         ataATTTTCATTGGTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTc                                                                                                                          <  2:335470/141‑1 (MQ=255)

              tttCATTGGTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTg                                                                                                                     <  1:568934/141‑1 (MQ=255)

                tCATTGGTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGaa                                                                                                                   <  1:186506/141‑1 (MQ=255)

                  aTTGGTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACg                                                                                                                 <  2:193974/141‑1 (MQ=255)

                   ttGGTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATAGATTGCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGc                                                                                                                >  2:267086/1‑141 (MQ=255)

                           gTTTTGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTATGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTg                                                                                                        <  2:365777/141‑1 (MQ=255)

                               tGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTc                                                                                                    >  1:426800/1‑141 (MQ=255)

                                  gTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTa                                                                                                 >  2:71920/1‑141 (MQ=255)

                                    tttAATTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATTGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAAt                                                                                               <  2:169117/141‑1 (MQ=255)

                                        aGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCaa                                                                                           <  1:47036/141‑1 (MQ=255)

                                            gCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGAGAACTGTTTCGCCTTCCATTGAACGCTCATTTTGCGTCTTAATCCAATCAt                                                                                       >  2:389345/1‑141 (MQ=255)

                                            gCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCGTTCCATTAAACGCTCAATTTGCGTCTTACTCCAATCAt                                                                                       >  1:532718/1‑141 (MQ=255)

                                                   aTGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAACTCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGACCGCTCAATTTGCGTCTTAATCCAATCATTTTGCtg                                                                                <  1:172196/141‑1 (MQ=255)

                                                                 ttAAAGGTACAAGTGTATGGTATAAATCTAACGTCTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAg                                                                  <  1:156183/141‑1 (MQ=255)

                                                                     aGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAg                                                              >  1:169875/1‑141 (MQ=255)

                                                                             gtgtATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTCCCGAAc                                                      >  2:307527/1‑141 (MQ=255)

                                                                             gtgtATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAAc                                                      <  1:448669/141‑1 (MQ=255)

                                                                                 aTGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACcaac                                                  <  1:254612/141‑1 (MQ=255)

                                                                                              aaCGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCATTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATGTTGCTGATTGATTTTGTAAGCGAGTGCCGAACCAACAATAATACAAaat                                     >  1:501936/1‑141 (MQ=255)

                                                                                                    ttgcggtatatTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACATAAATACACAATAATatg                               >  2:522917/7‑141 (MQ=255)

                                                                                                    tCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAatata                               >  2:387051/1‑140 (MQ=255)

                                                                                                      aCTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATatgat                             <  1:49898/141‑1 (MQ=255)

                                                                                                      aCTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATatgat                             >  1:358322/1‑141 (MQ=255)

                                                                                                         atatatTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATatgatgat                          >  2:64836/1‑141 (MQ=255)

                                                                                                          tatatTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATatgatgttg                         >  2:60136/1‑141 (MQ=255)

                                                                                                              tttCTATATTTTGATCATTAATGACAACAGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATGTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGAt                     <  1:396676/141‑1 (MQ=255)

                                                                                                                 ctcttttctGAGCATTAATGACTACTGTTTCGCCTTCCATTGAACGCTCACTTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCTAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTta                  <  1:197247/133‑1 (MQ=255)

                                                                                                                 cTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACAAAATAATATGATGATGAGATTta                  >  1:522012/1‑141 (MQ=255)

                                                                                                                    tatTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATAAGATGATCAGATTtaaaa               >  1:403929/1‑141 (MQ=255)

                                                                                                                       tttGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATAATGATGAGATTtaaaaata            >  1:180510/1‑141 (MQ=255)

                                                                                                                            tCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATaaaaaa       >  1:234986/1‑141 (MQ=255)

                                                                                                                             cATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATaaaaaaa      >  2:563166/1‑141 (MQ=255)

                                                                                                                                 aaTGACAACTGTTTCGCCTTCCATTGCACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTgg  >  2:341704/1‑141 (MQ=255)

                                                                                                                                 aaTGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAACCGAGTACCAAACCAACAATAATACACAATATTATGATGCTGAGATTTAAAAATAAAAAAACTgg  >  1:258746/1‑141 (MQ=255)

ATTAATATTATAATTTTCATTGGTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGG  >  CP000730/2027539‑2027808

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