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
A21 F63 I0 R1	92	32.2	718920	92.2%	662844	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	293,940	C→T	19.5%	intergenic (+57/‑471)	gatD → / → ispD2	zinc (Zn2+)‑binding dehydrogenase/2‑C‑methyl‑D‑erythritol 4‑phosphate cytidylyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	293,940	0	C	T	19.5%	74.4 / 10.1	35	intergenic (+57/‑471)	gatD/ispD2	zinc (Zn2+)‑binding dehydrogenase/2‑C‑methyl‑D‑erythritol 4‑phosphate cytidylyltransferase
Reads supporting (aligned to +/- strand): ref base C (15/13); new base T (4/3); total (19/16)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.79e-01

GTTAGAAAAAGGCCCGGAGACATTTGATAAATTAGTTAACAAGAAAGAACGATTTGATAAAGTCATGTTTACGATTTATTAGTATGCACCTTTGAGGACGAAAACGCTGGTATAGTTATAGCTATGAAAGTGCGAATGCCGTCTGGTCTATAGATACTATCGAAATAATTCATCTTCGAATATACGTTGATAAATAGCCGGTTTACTTGTGTGAAATATGCTTGTGAATCGGTTGTTTTGCATTTTGTATACTTAAAATGAGATGGCAATATTTGATAA  >  CP000730/293802‑294080

gTTAGAAAAAGGCCCGGAGACATTTGATAAATTAGTTAACAAGAAAGAACGATTTGATAAAGTCATGTTTACGATTTATTAGTATGCACCTTTGAGGACGAAAACGCTGGTATAGTTATAGCTATGAAAGTGCGAATGCCg                                                                                                                                            <  2:158626/141‑1 (MQ=255)

      aaaaGGCCCGGAGACATTTGGTAAATTAGTTAACAAGAAAGAACGATTTGATAAAGTCATGTTTACGATTTATTAGTATGCACCTTTGAGGCCGAAAACGCTGGTATAGTTATAGCTATGTAAGTGCGAATGCCGTCTGGt                                                                                                                                      <  2:40610/141‑1 (MQ=255)

       aaaGGCCCGGAGACATTTGATAAATTAGTTAACAAGAAAGAACGATTTGATAAAGTCATGTTTACGATTTATTAGTATGCACCTTTGAGGACGAAAACGCTGGTATAGTTATAGCTATGAAAGTGCGAATGCCGTCTGGTc                                                                                                                                     <  1:48608/141‑1 (MQ=255)

        aaGGCCCGGAGACATTTGATAAATTAGTTAACAAGAAAGAACGATTTGATAAAGTCATGTTTACGATTTATTAGTATGCACCTTTGAGGACGAAAACGCTGGTATAGTTATAGCTATGAAAGTGCGAATGCCGTCTGGTCt                                                                                                                                    >  1:94493/1‑141 (MQ=255)

        aaGGCCCGGAGACATTTGATAAATTAGTTAACAAGAAAGAACGATTTGATAAAGTCATGTTTACGATTTATTAGTATGCACCTTTGAGGACGAAAACGCTGGTATAGTTATAGCTATGAAAGTGCGAATGCCGTCTGGTCt                                                                                                                                    >  1:51311/1‑141 (MQ=255)

                gagaCATTTGATAAATTAGTTAACAAGAAAGAACGATTTGATAAAGTCATGTTTACGATTTATTAGTATGCACCTTTGAGGACGAAAACGCTGGTATGGTTATAGCTATGAAAGTGCGAATGCCGTCTGGTCTATAGATAc                                                                                                                            >  1:117227/1‑141 (MQ=255)

                                tattctaCAAGAAAGAACGATTTGATAAAGTCATGTTTACTATTTATTAGTAGGCACCTTTGAGGACGAAAACGCTTGTATAGTTATAGCTATGAAAGTGCGAATGTCGTCTGGTCTATAGATACTATCGAAATAATTCAt                                                                                                            <  2:205626/135‑1 (MQ=255)

                                 aGTTAACAAGAAAGAACGATTTGATAAAGTCATGTTTACGATTTATTAGTATGCACCTTTGAGGACGAAAACGCTGGTATAGTTATAGCTATGAAAGTGCGAATGCCGTCTGGTCTATAGATACTATCGAAATAATTCATc                                                                                                           >  1:61912/1‑141 (MQ=255)

                                 aGTTAACAAGAAAGAACGATATGCTAAAGACATGTACATGATTTATTACTAGGCACCTTTTAGGACGAAAACGCTGGTATAGGTATAGCTATGTAAGTGCGAATGTCGTCTGGTCTATAGATACTATCGAAATAATTCATc                                                                                                           >  2:339021/1‑141 (MQ=255)

                                  gTTAACAAGAAAGAACGATTTGATAAAGTCATGTTTACGATTTATTAGTATGCACCTTTGAGGACGAAAACGCTGGTATAGTTATAGCTATGAAAGTGCGAATGCCGTCTGGTCTATAGATACTATCGAAATAATTCATCt                                                                                                          >  2:323627/1‑141 (MQ=255)

                                  gTTAACAAGAAAGAACGATTTGATAAAGTCATGTTTACGATTTATTAGTATGCACCTTTGAGGACGAAAACGCTGGTATAGTTATAGCTATGAAAGTGCGAATGCCGTCTGGTCTATAGATACTATCGAAATAATTCATCt                                                                                                          >  2:139907/1‑141 (MQ=255)

                                               aaCGATTTGATAAAGTCATGTTTACGATTTATTAGTATGCACCTTTGAGGACGAAAACGCTGGTATAGTTATAGCTATGAAAGTGCGAATGCCGTCTGGTCTATAGATACTATCGAAATAATTCATCTTCGAATATACGtt                                                                                             >  2:20949/1‑141 (MQ=255)

                                                 cGATTTGATAAAGTCATGTTTACGATTTATTAGTATGCACCTTTGAGGACGAAAACGCTGGTATAGTTATAGCTATCAAAGTGCGAATGTCGTCTGGTCTATAGATACTATCGAAATAATTCATCTTCGAATATACGTTGa                                                                                           >  2:259711/1‑141 (MQ=255)

                                                  gATTTGATAAAGTCATGTTTACGATTTATTAGTATGCACCTTTGAGGACGAAAACGCTGGTATAGTTATAGCTATGAAAGTGCGAATGCCGTCTGGTCTATAGATACTATCGAAATAATTCATCTTCGAATATACGTTGAt                                                                                          <  2:61912/141‑1 (MQ=255)

                                                   aTTTGATAAAGTCATGTTTACGATTTATTAGTATGCACCTTTGCGGACGAAAACGCTGGTATAGTTATAGCTATGAAAGTGCGAATGCCGTCTGGTCTATAGATACTATCGAACTAATTCATCTTCGAATATACGTTGATa                                                                                         >  2:310919/1‑141 (MQ=255)

                                                     tttataatatCATGTTTACGATTTATTAGTATGCACCTTTGAGGACGAAAACGCTGGTATAGTTATAGCTATGAAAGTGCGAATGCCGTCTGGTCTATAGATACTATCGAAATAATTCATCTTCGAATATACGTTGATaaa                                                                                       <  2:212781/132‑1 (MQ=255)

                                                              tCATGTTTACGATTTATTAGTATGCACCTTTGAGGACGAAAACGCTGGTATAGTTATAGCTATGAAAGTGCGAATGCCGTCTGGTCTATAGATACTATCGAAATAATTCATCTTCGAATATACGTTGATAAATAGCCGGtt                                                                              <  2:94493/141‑1 (MQ=255)

                                                              tCATGTTTACGATTTATTAGTATGCACCTTTGAGGACGAAAACGCTGGTATAGTTATAGCTATGAAAGTGCGAATGCCGTCTGGTCTATAGATACTATCGAAATAATTCATCTTCGAATATACGTTGATAAATAGCCGGtt                                                                              <  2:51311/141‑1 (MQ=255)

                                                                 tGTTTACGATTTATTAGTATGCACCTTTGAGGACGAAAACGCTGGTATAGTTATAGCTATGAAAGTGCGAATGCCGTCTGGTCTATAGATACTATCGAACTAATTCATCTTCGAATATACGTTGATAAATAGCCGGTTTAc                                                                           >  1:159855/1‑141 (MQ=255)

                                                                    ttACGATTTATTAGTATGCACCTTTGAGGACGAAAACGCTGGTATAGTTATAGCTGTGAAAGTGCGAATGCCGTCTGGTCTATAGATACTATCGAAATAATTCATCTTCGAATATACGTTGATAAATAGCCGGTTTACTtg                                                                        >  2:92068/1‑141 (MQ=255)

                                                                    ttACGATTTATTAGTATGCACCTTTGAGGACGAAAACGCTGGTATAGTTATAGCTATGAAAGTGCGAATGCCGTCTGGTCTATAGATACTATCGAAATAATTCATCTTCGAATATACGTTGATAAATAGCCGGTTTACTtg                                                                        <  2:248963/141‑1 (MQ=255)

                                                                                      cACCTTTGAGGACGAAAACGCTGGTATAGTTATAGCTATGAAAGTGCGAATGCCGTCTGGTCTATAGATACTATCGAAATAATTCATCTTCGAATATACGTTGATAAATAGCCGGTTTACTTGTGTGAAATATGCTTGTGa                                                      >  2:257510/1‑141 (MQ=255)

                                                                                       aCCTTTGAGGACGAAAACGCTGGTATAGTTATAGCTATGAAAGTGCGAGTGCCGTCGGGTCTATAGATACTATCGAAATAATTCATCTTCGAATATACGTTGATAAATAGCCGGTTTACTTGTGTGAAATATGCTTGTGaa                                                     <  1:264394/141‑1 (MQ=255)

                                                                                            tGAGGACGAAAACGCTGGTATAGTTATAGCTATGAAAGTGCGAATGCCGTCTGGTCTATAGATACTATCGAAATAATTCATCTTCGAATATACGTTGATAAATAGCCGGTTTACTTGTGTGAAATATGCTTGTGAATCGgt                                                <  1:254453/141‑1 (MQ=255)

                                                                                              aGGACGAAAACGCTGGTATAGTTATAGCTATGAAAGTGCGAATGCCGTCTGGTCTATAGATACTATCGAAATAATTCATCTTCGAATATACGTTGATAAATAGCCGGTTTACTTGTGTGAAATATGCTTGTGAATCGggtg                                              >  1:192155/1‑141 (MQ=255)

                                                                                                 aggAACACTCTGGTAGAGTTATATATATGAAAGTGCGAATGCCGTCTCGTCTATAGCTACTACCGAAATAATTCATCTTGGAATATACGTTGATATATTGCCGGTTTAATTGTGTGAAATATGCTTGTGAATCGGTTGttt                                           <  2:167312/139‑1 (MQ=255)

                                                                                                  cGAAAACGCTGGTATAGTTATAGCTATGAAAGTGCGAATGCCGTCTGGTCTATAGATACTATCGAAATAATTCATCTTCGAATATACGTTGATAAGTAGCCGGTTTACTTGTGTGAAATATGCTTGTGAATCGGTTGtttt                                          >  1:344675/1‑141 (MQ=255)

                                                                                                     ataCGCTTGTATAGTTATAGCTATGAAAGTGCGAATGCCGTCTGGTCTATAGATACTATCGAAATAATTCATCTTCGAATATACGTTGATAAATAGCCGGTTTACTTGTGTGAAATATGCTTGTGAATCGGTTGTTTCGCa                                       <  2:352201/139‑1 (MQ=255)

                                                                                                          cTGGTATAGTTATAGCTATGAAAGTGCGAATGCCGTCTGGTCTATAGATACTATCGAAATAATTCATCTTCGAATATACGTTGATAAATAGCCGGTTTACTTGTGTGAAATATGCTTGTGAATCGGTTGTTTTGCATTTTg                                  <  1:206656/141‑1 (MQ=255)

                                                                                                                      taGCTATGAAAGTGCGAATGTCGTCTGGTCTATAGATACTATCGAAATAATTCATCTTCGAATATACGTTGATAAATAGCCGGTTTACTTGTGTGAAATATGCTTGTGAATCGGTTGTTTTGCATTTTGTATACTTAAAAt                      >  1:90441/1‑141 (MQ=255)

                                                                                                                           aTGAAAGTGCGAATGTCGTCTGGTCTATAGATACTATCGAAATAATTCATCTTCGAATATACGTTGATAAATAGCCGGTTTACTTGTGTGAAATATGCTTGTGAATCGGTTGTTTTGCATTTTGTATACTTAAAATGAGAt                 <  1:22031/141‑1 (MQ=255)

                                                                                                                           aTGAAAGTGCGAATGCCGTCTGGTCTATAGATACTATCGAAATAATTCATCTTCGAATATACGTTGATAAATAGCCGGTTTACTTGTGTGAAATATGCTTGTGAATCGGTTGTTTTGCATTTTGTATACTTAAAATGAGAt                 >  1:318976/1‑141 (MQ=255)

                                                                                                                            tGAAAGTGCGAATGCCGTCTGGTCTATAGATACTATCGAAATAATTCATCTTCGAATATACGTTGATAAATAGCCGGTTTACTTGTGTGAAATATGCTTGTGAATCGGTTGTTTTGCATTTTGTATACTTAAAATGAGATg                >  2:90359/1‑141 (MQ=255)

                                                                                                                                aGTGCGAATGTCGTCTGGTCTATAGATACTATCGAAATAATTCATCTTCGAATATACGTTGATAAATAGCCGGTTTACTTGTGTGAAATATGCTTGTGAATCGGTTGTTTTGCATTTTGTATACTTAAATTGAGATGGGaa            >  2:97665/1‑141 (MQ=255)

                                                                                                                                    cGAATGTCGTCTGGTCTATAGATACTATCGAAATAATTCATCTTCGAATATACGTTGATAAATAGCCGGTTTACTTGTGTGAAATATGCTTGTGAATCGGTTGTTTTGCATTTTGTATACTTAAAATGAGATGGCAATAtt        <  1:339021/141‑1 (MQ=255)

                                                                                                                                          ccGTCTGGTCTATAGATACTATCGAAATAATTCATCTTCGAATATACGTTGATAAATAGCCGGTTTACTTGTGTGAAATATGCTTGTGAATCGGTTGTTTTGCATTTTGTATACTTAAAATGAGATGGCAATATTTGATaa  <  2:7912/141‑1 (MQ=255)

GTTAGAAAAAGGCCCGGAGACATTTGATAAATTAGTTAACAAGAAAGAACGATTTGATAAAGTCATGTTTACGATTTATTAGTATGCACCTTTGAGGACGAAAACGCTGGTATAGTTATAGCTATGAAAGTGCGAATGCCGTCTGGTCTATAGATACTATCGAAATAATTCATCTTCGAATATACGTTGATAAATAGCCGGTTTACTTGTGTGAAATATGCTTGTGAATCGGTTGTTTTGCATTTTGTATACTTAAAATGAGATGGCAATATTTGATAA  >  CP000730/293802‑294080

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A