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
A23 F59 I1 R1	22	28.7	559496	97.2%	543830	149.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP000730	2,337,959	C→T	intergenic (‑125/‑119)	adhR ← / → USA300HOU_2196	possible MerR family transcriptional regulator/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,337,959	0	C	T	96.8%	107.2 / NA	31	intergenic (‑125/‑119)	adhR/USA300HOU_2196	possible MerR family transcriptional regulator/hypothetical protein
Reads supporting (aligned to +/- strand): ref base C (0/0); major base T (22/8); minor base A (1/0); total (23/8)
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

TTCATTGCGACTATCCTTTCAGTTATGTTTGGTCGTCTAAAGTAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCT‑TTTTTAACATTTTACATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAATTATTTTAGTTGCAATTTTTGGGTGATGCGGAAAATTTGGGTGATCGAT  >  CP000730/2337830‑2338101

ttCATTGCGACTATCCTTTCAGTTATGTTTGGTCGTCTAAAGTAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCT‑TTTTTAACATTTTATATTTCATCGTTTTTAATTa                                                                                                                             <  2:189931/149‑1 (MQ=255)

                 ttCAGTTATGTTTGGTCGTCTAAAGTAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCT‑TTTTTAACATTTTATATTTCATCGTTTTAAAAAAAAAAAAAAATTGTATaa                                                                                                            <  2:82953/149‑1 (MQ=255)

                     gTTATGTTTGGTCGTCTAAAGTAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCT‑TTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTa                                                                                                        >  2:132369/1‑149 (MQ=255)

                     gTTATGTTTGGTCGTCTAAAGTAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCT‑TTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTa                                                                                                        >  1:169141/1‑149 (MQ=255)

                     gTTATGTTTGGTCGTCTAAAGTAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCT‑TTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTa                                                                                                        >  2:7222/1‑149 (MQ=255)

                         tGTTTGGTCGTCTAAAGTAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCT‑TTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAata                                                                                                    >  1:35144/1‑149 (MQ=255)

                         tGTTTGGTCGTCTAAAGTAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCT‑TTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAata                                                                                                    >  1:69534/1‑149 (MQ=255)

                           tttGGTCGTCTAAAGTAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTCTTATTAAC‑TTCTCTCTTTTATCGATATCAATTAATTTAAAAATTGTATAACTTCAATAtt                                                                                                  >  1:235441/1‑149 (MQ=255)

                           tttGGTCGTCTAAAGTAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCT‑TTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATAtt                                                                                                  >  1:20932/1‑149 (MQ=255)

                           tttGGTCGTCTAAAGTAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTAACACC‑TTATCAACATATAAAAACACATATATTTTCATTAGTTTAAAATTTGTATAACTTAAATAtt                                                                                                  >  1:235447/1‑149 (MQ=255)

                            ttGGTCGTCTAAAGTAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCT‑TTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATAttt                                                                                                 >  2:57936/1‑149 (MQ=255)

                                tcgtcTAAAGTAATGTTGCTTTACATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCT‑TTTTTTTTTTTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTaaaa                                                                                             >  2:62980/1‑149 (MQ=255)

                                    cTAAAGTAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCT‑TTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGat                                                                                         >  1:154157/1‑149 (MQ=255)

                                                     tatataTTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCT‑TTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGa                                                                        >  1:8317/1‑149 (MQ=255)

                                                     tatataTTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCT‑TTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGa                                                                        >  1:31551/1‑149 (MQ=255)

                                                          atTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCT‑TTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGataata                                                                   >  2:11943/1‑149 (MQ=255)

                                                          atTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCT‑TTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGataata                                                                   >  1:149481/1‑149 (MQ=255)

                                                           ttGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCT‑TTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAatat                                                                  >  1:269145/1‑149 (MQ=255)

                                                              tCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCT‑TTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTa                                                               >  2:90238/1‑149 (MQ=255)

                                                              tCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCT‑TTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTa                                                               >  2:267934/1‑149 (MQ=255)

                                                                            aTACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCT‑TTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAatt                                                 >  1:186885/1‑149 (MQ=255)

                                                                              aCTTCTTATTTTATTACTCAAATTTAAATTTGTCTCT‑TTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAattat                                               >  2:79391/1‑149 (MQ=255)

                                                                                   ttattttattACTCAAATTTAAATTTGTCTCT‑TTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAATTATTTTAg                                          >  2:50141/1‑149 (MQ=255)

                                                                                                                 tt‑tttttAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAATTATTTTAGTTGCAATTTTTGGGTGATGCGGAAAATTTg            <  2:71295/148‑1 (MQ=255)

                                                                                                                    tttttAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAATTATTTTAGTTGCAATTTTTGGGTGATGCGGAAAATTTggg          >  1:219171/1‑149 (MQ=255)

                                                                                                                       ttAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAATTATTTTAGTTGCAATTTTTGGGTGATGCGGAAAATTTGGGTGa       <  1:277544/149‑1 (MQ=255)

                                                                                                                        tAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAATTATTTTAGTTGCAATTTTTGGGTGATGCGGAAAATTTGGGTGAt      >  1:156245/1‑149 (MQ=255)

                                                                                                                         aaCATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAATTATTTTAGTTGCAATTTTTGGGTGATGCGGAAAATTTGGGTGATc     <  2:188984/149‑1 (MQ=255)

                                                                                                                           cATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAATTATTTTAGTTGCAATTTTTGGGTGATGCGGAAAATTTGGGTGATCGa   <  1:118142/149‑1 (MQ=255)

                                                                                                                            aTTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAATTATTTTAGTTGCAATTTTTGGGTGATGCGGAAAATTTGGGTGATCGAt  <  1:214664/149‑1 (MQ=255)

                                                                                                                            aTTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAATTATTTTAGTTGCAATTTTTGGGTGATGCGGAAAATTTGGGTGATCGAt  <  1:121725/149‑1 (MQ=255)

TTCATTGCGACTATCCTTTCAGTTATGTTTGGTCGTCTAAAGTAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCT‑TTTTTAACATTTTACATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAATTATTTTAGTTGCAATTTTTGGGTGATGCGGAAAATTTGGGTGATCGAT  >  CP000730/2337830‑2338101

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

GATK/CNVnator alignment

N/A