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
A9 F22 I0 R2	95	29.9	669916	92.3%	618332	139.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	2,337,959	C→T	13.2%	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	13.2%	90.4 / 3.4	36	intergenic (‑125/‑119)	adhR/USA300HOU_2196	possible MerR family transcriptional regulator/hypothetical protein
Reads supporting (aligned to +/- strand): ref base C (15/16); new base T (3/2); total (18/18)
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

TTTAGTTTTCATTGCGACTATCCTTTCAGTTATGTTTGGTCGTCTAAAGTAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTACATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAATTATTTTAGTTGCAATTTTTGGGTGATGCGGAAAATTTGGGTG  >  CP000730/2337823‑2338095

tttAGTTTTCATTGCGACTATCCTTTCAGTTATGTTTGGTCGTCTAAAGTAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATAttt                                                                                                                                      >  1:304099/1‑141 (MQ=255)

   aGTTTTCATTGCGACTATCCTTTCAGTTATGTTTGGTCGTCTAAAGTAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTACATTTCAt                                                                                                                                   >  2:202497/1‑141 (MQ=255)

   aGTTTTCATTGCGACTATCCTTTCAGTTATGTTTGGTCGTCTAAAGTAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTACATTTCAt                                                                                                                                   <  2:175557/141‑1 (MQ=255)

     ttttCATTGCGACTATCCTTTCAGTTATGTTTGGTCGTCTAAAGTAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTATCTATGTTAACATTTTACATTTCATCg                                                                                                                                 <  1:159656/141‑1 (MQ=255)

         cATTGCGACTATCCTTTCAGTTATGTTTGGTCGTCTAAAGTAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTAAAATTTAAATTTGTCTCTTTTTTAACATTTTACATTTCATCGtttt                                                                                                                             >  1:146448/1‑141 (MQ=255)

                aCTATCCTTTCAGTTATGTTTGGTCGTCTAAAGTAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTACATTTCATCGTTTTTaaagta                                                                                                                      <  2:45191/141‑5 (MQ=255)

                aCTATCCTTTCAGTTATGTTTGGTCGTCTAAAGCAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATGTTATTACTCATATTTAGATTTGTCTCTTTTTTAACATTTTACATTTCATCGTTTTTaaagta                                                                                                                      <  2:45174/141‑5 (MQ=255)

                       tttCAGTTATGTTTGGTCGTCTAAAGTAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTACATTTCATCGTTTTTAATTACTTTaaaa                                                                                                               <  1:213609/141‑1 (MQ=255)

                         tCAGTTATGTTTGGTCGTCTAAAGTAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTACATTTCATCGTTTTTAATTACTTTAAAAAt                                                                                                             >  1:121476/1‑141 (MQ=255)

                             ttATGTTTGGTCGTCTAAAGTAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGta                                                                                                         >  1:213270/1‑141 (MQ=255)

                                                   aTGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTACATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGat                                                                                   >  1:254947/1‑141 (MQ=255)

                                                     gTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTACATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGatat                                                                                 >  1:232763/1‑141 (MQ=255)

                                                            tatataTTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTACATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACt                                                                          >  1:185583/1‑141 (MQ=255)

                                                             atatatTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCACATTTAAATTTGTCTCTATTTTAACATTTTATATTTCATCGTTTTTAATTTCTTTATGAATTGTATAACTGAAATATTTAAAATGATATAATCACTa                                                                         <  2:196421/141‑1 (MQ=255)

                                                               atatTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAg                                                                       >  2:170470/1‑141 (MQ=255)

                                                                  ttGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTACATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGAtt                                                                    <  2:173985/141‑1 (MQ=255)

                                                                     tCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTACATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGat                                                                 >  1:111725/1‑141 (MQ=255)

                                                                           tCGTTTGAATACTTCATATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTACATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATTACTAATATTCATAAtttt                                                           >  2:267204/1‑141 (MQ=255)

                                                                                     aCTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTACATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTAATTTTTTg                                                 <  1:4399/141‑1 (MQ=255)

                                                                                                    aCTCAAATTTAAATTTGTCTCTTTTTTAACATTTTACATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTAATTTTTTGAAACTTATTTTAGtt                                  <  2:73545/141‑1 (MQ=255)

                                                                                                     cTCAAATTTAAATTTGTCTCTTTTTTAACATTTTACATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAATTATTTTAGTTg                                 <  2:137210/141‑1 (MQ=255)

                                                                                                     cTCAAATTTAAATTTAGATCAAGCATAACTTTTTACATTTCATAAATTTTAATTACTTTAAAAATTGTATAACTTACATATGTTAAATGATATAATCGTTAATGTTGATAATATTTACTTTTCTGAAAATTATATTTGtct                                 >  2:62298/1‑139 (MQ=255)

                                                                                                      tCAAATTTAAATTTGTCTCTTTTTTAACATTTTACATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAATTATTTTAGTTGc                                <  2:87591/141‑1 (MQ=255)

                                                                                                      tCAAATTTAAATTTGTCTCTTTTTTAACATTTTACATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAATTATTTTAGTTGc                                <  1:279174/141‑1 (MQ=255)

                                                                                                      tCAAATTTAAATTTGTCTCTTTTTTAACATTTTACATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAATTATTTTAGTTGc                                <  2:236648/141‑1 (MQ=255)

                                                                                                      tCAAATTTAAATTTGTCTCTTTTTTAACATTTTACATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAATTATTTTAGTTGc                                <  2:85079/141‑1 (MQ=255)

                                                                                                       cAAATTTAAATTTGTCTCTTTTTTAACATTTTACATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAATTATTTTAGTTGCa                               >  2:79738/1‑141 (MQ=255)

                                                                                                               aatttGTCTCTTTTTTAACATTTTACATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAATTATTTTAGTTGCAATTTTTgg                       >  2:108059/1‑141 (MQ=255)

                                                                                                               aatttGTCTCTTTTTTAACATTTTACATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAATTATTTTAGTTGCAATTTTTgg                       >  1:317366/1‑141 (MQ=255)

                                                                                                                 tttGTCTCTTTTTTAACATTTTACATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAATTATTTTAGTTGCAATTTTTGGGt                     >  1:94749/1‑141 (MQ=255)

                                                                                                                 tttGTCTCTTTTTTAACATTTTACATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAATTATTTTAGTTGCAATTTTTGGGt                     <  1:97077/141‑1 (MQ=255)

                                                                                                                       tctTTTTTAACATTTTACATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAATTATTTTAGTTGCAATTTTTGGGTGATGCg               >  2:262739/1‑141 (MQ=255)

                                                                                                                                aCATTTTACATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAATTATTTTAGTTGCAATTTTTGGGTGATGCGGAAAATTTg      <  2:257317/141‑1 (MQ=255)

                                                                                                                                 cATTTTACATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAATTATTTTAGTTGCAATTTTTGGGTGATGCGGAAAATTTgg     <  2:72378/141‑1 (MQ=255)

                                                                                                                                   ttttATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAATTATTTTAGTTGCAATTTTTGGGTGATGCGGAAAATTTGGGt   <  2:213270/141‑1 (MQ=255)

                                                                                                                                    tttACATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAATTATTTTAGTTGCAATTTTTGGGTGATGCGGAAAATTTGGGTg  >  1:319992/1‑141 (MQ=255)

TTTAGTTTTCATTGCGACTATCCTTTCAGTTATGTTTGGTCGTCTAAAGTAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTACATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAATTATTTTAGTTGCAATTTTTGGGTGATGCGGAAAATTTGGGTG  >  CP000730/2337823‑2338095

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A