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
A1 F21 I0 R2	308	27.9	1975068	96.7%	1909890	67.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	3,442,070	A→G	40.0%	T497A (ACG→GCG)	thiC →	thiamin (pyrimidine moiety) biosynthesis protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	3,442,070	0	A	G	40.0%	33.9 / 70.9	60	T497A (ACG→GCG)	thiC	thiamin (pyrimidine moiety) biosynthesis protein
Reads supporting (aligned to +/- strand): ref base A (29/7); new base G (12/12); total (41/19)
Fisher's exact test for biased strand distribution p-value = 2.23e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.49e-01

TCACGTCGGGGATTGGTGCGGCGATGATTGGCTGGTTTGGCTGCGCGATGCTCTGTTACGTAACGCCAAAAGAGCATCTGGGTCTGCCCAATAAAGAAGATGTTAAGCAGGGGCTTATCACCTAT  >  W3110S.gb/3442008‑3442132

tCACGTCGGGGATTGGTGCGGCGATGATTGGCTGGTTTGGCTGCGCGATGCTCTGTTACGTAACGCCaa                                                          >  1:544257/1‑69 (MQ=255)

tCACGTCGGGGATTGGTGCGGCGATGATTGGCTGGTTTGGCTGCGCGATGCTCTGTTACGTAACGCCaa                                                          >  1:1180149/1‑69 (MQ=255)

tCACGTCGGGGATTGGTGCGGCGATGATTGGCTGGTTTGGCTGCGCGATGCTCTGTTACGTAACGCCaa                                                          >  1:1025228/1‑69 (MQ=255)

tCACGTCGGGGATTGGTGCGGCGATGATTGGCTGGTTTGGCTGCGCGATGCTCTGTTACGTAACGCCaa                                                          >  1:1244621/1‑69 (MQ=255)

tCACGTCGGGGATTGGTGCGGCGATGATTGGCTGGTTTGGCTGCGCGATGCTCTGTTACGTAACGCCaa                                                          >  1:22691/1‑69 (MQ=255)

tCACGTCGGGGATTGGTGCGGCGATGATTGGCTGGTTTGGCTGCGCGATGCTCTGTTACGTAACGCCaa                                                          >  1:1924110/1‑69 (MQ=255)

 cACGTCGGGGATTGGTGCGGCGATGATTGGCTGGTTTGGCTGCGCGATGCTCTGTTACGTAGCGCCaa                                                          >  1:611812/1‑68 (MQ=255)

 cACGTCGGGGATTGGTGCGGCGATGATTGGCTGGTTTGGCTGCGCGATGCTCTGTTACGTAGCGCCaa                                                          >  1:1773655/1‑68 (MQ=255)

 cACGTCGGGGATTGGTGCGGCGATGATTGGCTGGTTTGGCTGCGCGATGCTCTGTTACGTAGCGCCaa                                                          >  1:313263/1‑68 (MQ=255)

 cACGTCGGGGATTGGTGCGGCGATGATTGGCTGGTTTGGCTGCGCGATGCTCTGTTACGTAGCGCCaa                                                          >  1:1293404/1‑68 (MQ=255)

 cACGTCGGGGATTGGTGCGGCGATGATTGGCTGGTTTGGCTGCGCGATGCTCTGTTACGTAGCGCCaa                                                          >  1:1437542/1‑68 (MQ=255)

 cACGTCGGGGATTGGTGCGGCGATGATTGGCTGGTTTGGCTGCGCGATGCTCTGTTACGTAGCGCCaa                                                          >  1:1315845/1‑68 (MQ=255)

 cACGTCGGGGATTGGTGCGGCGATGATTGGCTGGTTTGGCTGCGCGATGCTCTGTTACGTAGCGCCaa                                                          >  1:228736/1‑68 (MQ=255)

 cACGTCGGGGATTGGTGCGGCGATGATTGGCTGGTTTGGCTGCGCGATGCTCTGTTACGTAGCGCCaa                                                          >  1:206737/1‑68 (MQ=255)

 cACGTCGGGGATTGGTGCGGCGATGATTGGCTGGTTTGGCTGCGCGATGCTCTGTTACGTAGCGCCaa                                                          >  1:87303/1‑68 (MQ=255)

 cACGTCGGGGATTGGTGCGGCGATGATTGGCTGGTTTGGCTGCGCGATGCTCTGTTACGTAGCGCCa                                                           >  1:1421013/1‑67 (MQ=255)

 cACGTCGGGGATTGGTGCGGCGATGATTGGCTGGTTTGGCTGCGCGATGCTCTGTTACGTAACGCCaa                                                          >  1:1588832/1‑68 (MQ=255)

 cACGTCGGGGATTGGTGCGGCGATGATTGGCTGGTTTGGCTGCGCGATGCTCTGTTACGTAACGCCaa                                                          >  1:68938/1‑68 (MQ=255)

 cACGTCGGGGATTGGTGCGGCGATGATTGGCTGGTTTGGCTGCGCGATGCTCTGTTACGTAACGCCaa                                                          >  1:53560/1‑68 (MQ=255)

    gTCGGGGATTGGTGCGGCGATGATTGGCTGGTTTGGCTGCGCGATGCTCTGTTACGTAACGCCAAAAGAGc                                                    <  1:1293902/71‑1 (MQ=255)

    gTCGGGGATTGGTGCGGCGATGATTGGCTGGTTTGGCTGCGCGATGCTCTGTTACGTAACGCCAAAAGAGc                                                    <  1:1188478/71‑1 (MQ=255)

     tCGGGGATTGGTGCGGCGATGATTGGCTGGTTTGGCTGCGCGATGCTCTGTTACGTAACGCCAAAAGAGCa                                                   <  1:1770166/71‑1 (MQ=255)

                         gatTGGCTGGTTTGGCTGCGCGATGCTCTGTTACGTAACGCCAAAAGAGCATCTGGGTCTGCCCAATa                                  >  1:546741/1‑68 (MQ=255)

                         gatTGGCTGGTTTGGCTGCGCGATGCTCTGTTACGTAACGCCAAAAGAGCATCTGGGTCTGCCCAATa                                  >  1:1084070/1‑68 (MQ=255)

                          atTGGCTGGTTTGGCTGCGCGATGCTCTGTTACGTAGCGCCAAAAGAGCATCTGGGTCTGCCCAATAaag                               <  1:1379884/70‑1 (MQ=255)

                          atTGGCTGGTTTGGCTGCGCGATGCTCTGTTACGTAGCGCCAAAAGAGCATCTGGGTCTGCCCAATAaag                               <  1:339620/70‑1 (MQ=255)

                            tGGCTGGTTTGGCTGCGCGATGCTCTGTTACGTAACGCCAAAAGAGCATCTGGGTCTGCCCAATAaag                               >  1:862249/1‑68 (MQ=255)

                                     tGGCTGCGCGATGCTCTGTTACGTAACGCCAAAAGAGCATCTGGGTCTGCCCAATAAAGAAGATGTTAAg                    >  1:1567791/1‑70 (MQ=255)

                                     tGGCTGCGCGATGCTCTGTTACGTAACGCCAAAAGAGCATCTGGGTCTGCCCAATAAAGAAGATGTTAAg                    >  1:1417783/1‑70 (MQ=255)

                                     tGGCTGCGCGATGCTCTGTTACGTAACGCCAAAAGAGCATCTGGGTCTGCCCAATAAAGAAGATGTTAAg                    >  1:1408624/1‑70 (MQ=255)

                                     tGGCTGCGCGATGCTCTGTTACGTAACGCCAAAAGAGCATCTGGGTCTGCCCAATAAAGAAGATGTTAAg                    >  1:55272/1‑70 (MQ=255)

                                     tGGCTGCGCGATGCTCTGTTACGTAACGCCAAAAGAGCATCTGGGTCTGCCCAATAAAGAAGATGTTAAg                    >  1:874548/1‑70 (MQ=255)

                                     tGGCTGCGCGATGCTCTGTTACGTAACGCCAAAAGAGCATCTGGGTCTGCCCAATAAAGAAGATGTTAAg                    >  1:1252359/1‑70 (MQ=255)

                                     tGGATGCGCGATGCTCTGTTACGTAACGCCAAAAGAGCATCTGGGTCTGCCCAATaa                                 >  1:1318932/1‑57 (MQ=255)

                                       gCTGCGCGATGCTCTGTTACGTAACGCCAAAAGAGCATCTGGGTCTGCCCAATAAAGAAGATGTTAAGCa                  <  1:1679440/70‑1 (MQ=255)

                                       gCTGCGCGATGCTCTGTTACGTAACGCCAAAAGAGCATCTGGGTCTGCCCAATAAAGAAGATGTTAAGCa                  <  1:618191/70‑1 (MQ=255)

                                           cgcgATGCTCTGTTACGTAACGCCAAAAGAGCATCTGGGTCTGCCCAATAAAGAAGATGTTAAGCAgggg              <  1:205851/70‑1 (MQ=255)

                                           cgcgATGCTCTGTTACGTAACGCCAAAAGAGCATCTGGGTCTGCCCAATAAAGAAGATGTTAAGCAgggg              <  1:1097609/70‑1 (MQ=255)

                                                tGCTCTGTTACGTAGCGCCAAATGAGCATCTGGGTCTGCCCAATAAAGAAGATGTTAAGCAgggg              <  1:346098/65‑1 (MQ=255)

                                                tGCTCTGTTACGTAGCGCCAAAAGAGCATCTTGGTCTGCCCAATAAAGAAGATGTTAAGCAgggg              <  1:1791357/65‑1 (MQ=255)

                                                tGCTCTGTTACGTAGCGCCAAAAGAGCATCTGGGTCTGCCCAATAAAGAAGATGTTAAGCAgggg              <  1:88185/65‑1 (MQ=255)

                                                tGCTCTGTTACGTAGCGCCAAAAGAGCATCTGGGTCTGCCCAATAAAGAAGATGTTAAGCAgggg              <  1:66757/65‑1 (MQ=255)

                                                tGCTCTGTTACGTAGCGCCAAAAGAGCATCTGGGTCTGCCCAATAAAGAAGATGTTAAGCAgggg              <  1:901281/65‑1 (MQ=255)

                                                tGCTCTGTTACGTAGCGCCAAAAGAGCATCTGGGTCTGCCCAATAAAGAAGATGTTAAGCAgggg              <  1:521953/65‑1 (MQ=255)

                                                tGCTCTGTTACGTAGCGCCAAAAGAGCATCTGGGTCTGCCCAATAAAGAAGATGTTAAGCAgggg              <  1:1919941/65‑1 (MQ=255)

                                                tGCTCTGTTACGTAGCGCCAAAAGAGCATCTGGGTCTGCCCAATAAAGAAGATGTTAAGCAgggg              <  1:1898702/65‑1 (MQ=255)

                                                tGCTCTGTTACGTAGCGCCAAAAGAGCATCTGGGTCTGCCCAATAAAGAAGATGTTAAGCAgggg              <  1:1655363/65‑1 (MQ=255)

                                                 gCTCTGTTACGTAGCGCCAAAAGAGCATCTGGGTCTGCCCAATAAAGAAGATGTTAAGCAgggg              <  1:410527/64‑1 (MQ=255)

                                                  ctctGTTACGTAGCGCCAAAAGAGCATCTGGGTCTGCCCAATAAAGAAGATGTTAAGCAGGGGCTTATCAc      >  1:727355/1‑71 (MQ=255)

                                                  ctctGTTACGTAGCGCCAAAAGAGCATCTGGGTCTGCCCAATAAAGAAGATGTTAAGCAGGGGCTTATCAc      >  1:1426734/1‑71 (MQ=255)

                                                        tACGTAACGCCAAAAGAGCATCTGGGTCTGCCCAATAAAGAAGATGTTAAGCAGGGGCTTATCACCtat  >  1:515742/1‑69 (MQ=255)

                                                        tACGTAACGCCAAAAGAGCATCTGGGTCTGCCCAATAAAGAAGATGTTAAGCAGGGGCTTATCACCtat  >  1:499148/1‑69 (MQ=255)

                                                        tACGTAACGCCAAAAGAGCATCTGGGTCTGCCCAATAAAGAAGATGTTAAGCAGGGGCTTATCACCtat  >  1:355117/1‑69 (MQ=255)

                                                        tACGTAACGCCAAAAGAGCATCTGGGTCTGCCCAATAAAGAAGATGTTAAGCAGGGGCTTATCACCtat  >  1:200429/1‑69 (MQ=255)

                                                        tACGTAACGCCAAAAGAGCATCTGGGTCTGCCCAATAAAGAAGATGTTAAGCAGGGGCTTATCACCtat  >  1:1611770/1‑69 (MQ=255)

                                                        tACGTAACGCCAAAAGAGCATCTGGGTCTGCCCAATAAAGAAGATGTTAAGCAGGGGCTTATCACCtat  >  1:1488566/1‑69 (MQ=255)

                                                        tACGTAACGCCAAAAGAGCATCTGGGTCTGCCCAATAAAGAAGATGTTAAGCAGGGGCTTATCACCtat  >  1:1356261/1‑69 (MQ=255)

                                                        tACGTAACGCCAAAAGAGCATCTGGGTCTGCCCAATAAAGAAGATGTTAAGCAGGGGCTTATCACCtat  >  1:1336253/1‑69 (MQ=255)

                                                        tACGTAACGCCAAAAGAGCATCTGGGTCTGCCCAATAAAGAAGATGTTAAGCAGGGGCTTATCACCtat  >  1:1185013/1‑69 (MQ=255)

                                                        tACGTAACGCCAAAAGAGCATCTGGGTCTGCCCAATAAAGAAGATGTTAAGCAGGGGCTTATCACCta   >  1:1947230/1‑68 (MQ=255)

TCACGTCGGGGATTGGTGCGGCGATGATTGGCTGGTTTGGCTGCGCGATGCTCTGTTACGTAACGCCAAAAGAGCATCTGGGTCTGCCCAATAAAGAAGATGTTAAGCAGGGGCTTATCACCTAT  >  W3110S.gb/3442008‑3442132

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A