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
A19 F74 I1 R2	13	29.8	697290	91.1%	635231	133.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP000730	2,026,955	G→A	T331I (ACA→ATA)	vraS ←	sensor histidine kinase VraS

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,026,955	0	G	A	96.3%	81.7 / NA	27	T331I (ACA→ATA)	vraS	sensor histidine kinase VraS
Reads supporting (aligned to +/- strand): ref base G (0/0); major base A (18/8); minor base C (1/0); total (19/8)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACTACTTCAATATCACTTTGCGTTGATAGATAACTTGAAATTCCTATACGTACCATTTCATGATCATCCACAAACAATACTTTAATCGTCATACGAATCCTCCTTATTTAAAGGTGCTTTCACCTCGATACGTGTACCTGAATCTGGCAATGATACAATATGG‑AACGTTGCACCAATTTCCAAAGCTCTTTCACGCATATTTTTAAGTCCATAACTTTGTTCTAATTTTTCATCAACATTAAAACCTTTACCATTATCTTGAATTCT  >  CP000730/2026822‑2027088

actactTCAATATCACTTTGCGTTGATAGATAACTTGAAATTCCTATACGTACCATTTCATGATCATCCACAAACAATACTTTAATCGTCATACGAATCCTCCTTATTTAAAGGTGCTTTCACCTCGATACGTATACCTGa                                                                                                                                 <  1:20455/141‑1 (MQ=255)

      tCAATATCACTTTGCGTTGATAGATAACTTGAAATTCCTATACGTACCATTTCATGATCATCCACAAACAATACTTTAATCGTCATACGAATCCTCCTTATTTAAAGGTGCTTTCACCTCGATACGTATACCTGAATCTgg                                                                                                                           <  2:170541/141‑1 (MQ=255)

      tCAATATCACTTTGCGTTGATAGATAACTTGAAATTCCTATACGTACCATTTCATGATCATCCACAAACAATACTTTAATCGTCATACGAATCCTCCTTATTTAAAGGTGCTTTCACCTCGATACGTATACCTGAATCTgg                                                                                                                           >  1:205686/1‑141 (MQ=255)

                     gTTGATAGATAACTTGAAATTCCTATACGTACCATTTCATGATCATCCACAAACAATACTTTAATCGTCATACGAATCCTCCTTATTTAAAGGTGCTTTCACCTCGATACGTATACCTGAATCTGGCAATGATACAATATg                                                                                                            >  1:158931/1‑141 (MQ=255)

                     gTTGATAGATAACTTGAAATTCCTATACGTACCATTTCATGATCATCCACAAACAATACTTTAATCGTCATACGAATCCTCCTTATTTAAAGGTGCTTTCACCTCGATACGTATACCTGAATCTGGCAATGATACAATATg                                                                                                            >  1:99014/1‑141 (MQ=255)

                      ttGATAGATAACTTGAAATTCCTATACGTACCATTTCATGATCATCCACAAACAATACTTTAATCGTCATACGAATCCTCCTTATTTAAAGGTGCTTTCACCTCGATACGTATACCTGAATCTGGCAATGATACAATATgg                                                                                                           <  1:273736/141‑1 (MQ=255)

                               aaCTTGAAATTCCTATACGTACCATTTCATGATCATCCACAAACAATACTTTAATCGTCATACGAATCCTCCTTATTTAAAGGTGCTTTCACCTCGATACGTATACCTGAATCTGGCAATGATACAATATGG‑AACGTTGCa                                                                                                 <  2:198803/141‑1 (MQ=255)

                                  ttGAAATTCCTATACGTACCATTTCATGATCATCCACAAACAATACTTTAATCGTCATACGAATCCTCCTTATTTAAAGGTGCTTTCACCTCGATACGTATACCTGAATCTGGCAATGATACAATATGG‑AACGTTGCACCa                                                                                              >  1:157810/1‑141 (MQ=255)

                                     aaaTTCCTATACGTACCATTTCATGATCATCCACAAACAATACTTTAATCGTCATACGAATCCTCCTTATTTAAAGGTGCTTTCACCTCGATACGTATACCTGAATCTGGCAATGAAAC‑ATCTGGTAACGTTGCACCAAtt                                                                                           >  1:177937/1‑141 (MQ=255)

                                      aaTTCCTATACGTACCATTTCATGATCATCCACAAACAATACTTTAATCGTCATACGAATCCTCCTTATTTAAAGGTGCTTTCACCTCGATACGTATACCTGAATCTGGCAATGATACAATATGG‑AACGTTGCACCAAttt                                                                                          >  1:153670/1‑141 (MQ=255)

                                                cGTACCATTTCATGATCATCCACAAACAATACTTTAATCGTCATACGAATCCTCCTTATTTAAAGGTGCTTTCACCTCGATACGTATACCt                                                                                                                                   <  2:94999/91‑1 (MQ=255)

                                                cGTACCATTTCATGATCATCCACAAACAATACTTTAATCGTCATACGAATCCTCCTTATTTAAAGGTGCTTTCACCTCGATACGTATACCt                                                                                                                                   >  1:94999/1‑91 (MQ=255)

                                                    ccATTTCATGATCATCCACAAACAATACTTTAATCGTCATACGAATCCTCCTTATTTTATGTTGTTCTGGCCCGGATTCGGATGCCTGAATCTGGCAATGATACAATATGG‑AACGTTGCACCAATTTCCAAAGCTCTTTCa                                                                            >  1:155659/1‑141 (MQ=255)

                                                    ccATTTCATGATCATCCACAAACAATACTTTAATCGTCATACGAATCCTCCTTATTTAAAGGTGCTTTCACCTCGATACGTATACCTGAATCTGGCAATGATACAATATGG‑AACGTTGCACCAATTTCCAAAGCTCTTTCa                                                                            >  1:321891/1‑141 (MQ=255)

                                                      aTTTCATGATCATCCACAAACAATACTTTAATCGTCATACGAATCCTCCTTATTTAAAGGTGCTTTCACCTCGATACGTATACCTGAATCTGGCAATGATACAATATGG‑AACGTTGCACCAATTTCCAAAGCTCTTTCACg                                                                          <  1:66523/141‑1 (MQ=255)

                                                          cATGATCATCCACAAACAATACTTTAATCGTCATACGAATCCTCCTTATTTAAAGGTGCTTTCACATCGATACGTATACCTGAATCTGGCATTGATACAATATGG‑ATCGTTGCACCAATTTCTAAAGCTCTTTCACGCcta                                                                      >  1:286785/1‑141 (MQ=255)

                                                           aTGATCATCCACAAACAATACTTTAATCGTCATACGAATCCTCCTTATTTAAAGGTGCTTTCACCTCGATACGTATACCTGAATCTGGCAATGATACAATATGG‑AACGTTGCACCAATTTCCAAAGCTCTTTCACGCatat                                                                     >  1:278020/1‑141 (MQ=255)

                                                                              aCTTTAATAGACATACGAATCCTCCTTATTTAAAGGTGATTTCACATCGCTCCGTCTACCTGAATCTGGCAATGATACAATATGG‑AACGTTGCACCAATTTCCAAAGCTCTTTCACGCATATTTTTAAGTCAATCACttta                                                  >  2:293379/1‑140 (MQ=255)

                                                                                    aTCGTCATACGAATCCTCCTTATTTAAAGGTGCTTTCACCTCGATACGTATACCTGAATCTGGCAATGATACAATATGG‑AACGTTGCACCAATTTCCAAAGCTCTTTCACGCATATTTTTAAGTCCATAACTTTGTTCTaa                                            >  1:254755/1‑141 (MQ=255)

                                                                                         cATACGAATCCTCCTTATTTAAAGGTGCTTTCACCTCGATACGTATACCTGAATCTGGCAATGATACAATATGG‑AACGTTGCACCAATTTCCAAAGCTCTTTCACGCATATTTTTAAGTCCATAACTTTGTTCTAAttttt                                       >  1:10628/1‑141 (MQ=255)

                                                                                         cATACGAATCCTCCTTATTTAAAGGTGCTTTCACCTCGATACGTATACCTGAATCTGGCAATGATACAATATGG‑AACGTTGCACCAATTTCCAAAGCTCTTTCACGCATATTTTTAAGTCCATAACTTTGTTCTAAttttt                                       >  1:246420/1‑141 (MQ=255)

                                                                                            aCGAATCCTCCTTATTTAAAGGTGCTTTCACGTCGATACGTATACCTGAATCTGGCAATGATACAATATGG‑AACGTTGCACCAATTTCCAAAGCTCTTTCACGCATCTTTTTAAGTCCATAACTTTGTTCTAATTTTtcaa                                    >  2:174479/1‑140 (MQ=255)

                                                                                               agtcctccTTGTTTAAATGTGCGTTCTCCTCGATACGTATACCTGAATCGCGAAATGATACAATATGG‑AACCTTGCACCAATTTCCCAAGCCCTTTCACGCATATTTTTAAGTCCATAACTATTTTCTAATTTTtcatcca                                 <  2:137103/139‑3 (MQ=255)

                                                                                                     cctTATTTAAAGGTGCTTTCACCTCGATACGTATACCTGAATCTGGCAATGATACAATATGG‑AACGTTGCACCAATTTCCAAAGCTCTTTCACGCATATTTTTAAGTCCATAACTTTGTTCTAATTTTTCATCAACATTaa                           <  1:342059/141‑1 (MQ=255)

                                                                                                             aaaGGTGCTTTCACCTCGATACGTATACCTGAATCTGGCAATGATACAATATGG‑AACGTTGCACCAATTTCCAAAGCTCTTTCACGCATATTTTTAAGTCCATAACTTTGTTCTAATTTTTCATCAACATTAAAACCTTTa                   >  1:58008/1‑141 (MQ=255)

                                                                                                                   gCTTTCACCTCGATACGTATACCTGAATCTGGCAATGATACAATATGG‑AACGTTGCACCAATTTCCAAAGCTCTTTCACGCATATTTTTAAGTCCATAACTTTGTTCTAATTTTTCATCAACATTAAAACCTTTACCATTa             >  1:14856/1‑141 (MQ=255)

                                                                                                                              gATACGTATACCTGAATCTGGCAATGATACAATATGG‑AACGTTGCACCAATTTCCAAAGCTCTTTCACGCATATTTTTAAGTCCATAACTTTGTTCTAATTTTTCATCAACATTAAAACCTTTACCATTATCTTGAATtct  >  2:266706/1‑141 (MQ=255)

ACTACTTCAATATCACTTTGCGTTGATAGATAACTTGAAATTCCTATACGTACCATTTCATGATCATCCACAAACAATACTTTAATCGTCATACGAATCCTCCTTATTTAAAGGTGCTTTCACCTCGATACGTGTACCTGAATCTGGCAATGATACAATATGG‑AACGTTGCACCAATTTCCAAAGCTCTTTCACGCATATTTTTAAGTCCATAACTTTGTTCTAATTTTTCATCAACATTAAAACCTTTACCATTATCTTGAATTCT  >  CP000730/2026822‑2027088

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A