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
A6 F1 I1 R1	750	51.0	2595496	93.6%	2429384	106.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,548,360	C→T	D320D (GAC→GAT)	fdnG →	formate dehydrogenase‑N, alpha subunit, nitrate‑inducible

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,548,360	0	C	T	94.4%	98.6 / ‑1.4	36	D320D (GAC→GAT)	fdnG	formate dehydrogenase‑N, alpha subunit, nitrate‑inducible
Reads supporting (aligned to +/- strand): ref base C (1/1); new base T (16/18); total (17/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.67e-01

TCGTTCCGGTACGGACATTACGTTCCTGTCTGGCGTTTTGCGCTACCTGATCGAAAACAACAAAATCAACGCCGAATACGTTAAGCATTACACCAACGCCAGCCTGCTGGTGCGTGATGATTTTGCTTTCGAAGACGGTCTGTTCAGCGGCTACGACGCTGAAAAACGTCAATACGATAAATCGTCCTGGAACTATCAGCTCGATGAAAACGGCTATGCGAAACGCGATGAAACACTGACTCATCCGCGC  >  NC_000913/1548225‑1548474

tCGTTCCGGTACGGACATTACGTTCCTGTCTGGCGTTTTGCGCTACCTGATCGAAAACAACAAAATCAACGCCGAATACGTTAAGCATTACACCGACGCCAGCCTGCTGGTGCGTGATGATTTTGCTTTCGAAGATGGt                                                                                                                 <  2:425808/139‑1 (MQ=255)

           cGGACATTACGTTCCTGTCTGGCGTTTTGCGCTACCTGATCGAAAACAACAAAATCAACGCCGAATACGTTAAGCATTACACCAACGCCAGCCTGCTGGTGCGTGATGATTTTGCTTTCGAAGATGGTCTGTTCAGCgg                                                                                                      >  1:173742/1‑139 (MQ=255)

              aCATTACGTTCCTGTCTGGCGTTTTGCGCTACCTGATCGAAAACAACAAAATCAACGCCGAATACGTTAAGCATTACACCAACGCCAGCCTGCTGGTGCGTGATGATTTTGCTTTCGAAGATGGTCTGTTCAGCGGCTa                                                                                                   <  2:173742/139‑1 (MQ=255)

                        ccTGTCTGGCGTTTTGCGCTACCTGATCGAAAACAACAAAATCAACGCCGAATACGTTAAGCATTACACCAACGCCAGCCTGCTGGTGCGTGATGATTTTGCTTTCGAAGACGGTCTGTTCAGCGGCTACGACGCTGaa                                                                                         >  2:1278610/1‑139 (MQ=255)

                          tGTCTGGCGTTTTGCGCTACCTGATCGAAAACAACAAAATCAACGCCGAATACGTTAAGCATTACACCAACGCCAGCCTGCTGGTGCGTGATGATTTTGCTTTCGAAGATGGt                                                                                                                 <  2:821640/113‑1 (MQ=255)

                          tGTCTGGCGTTTTGCGCTACCTGATCGAAAACAACAAAATCAACGCCGAATACGTTAAGCATTACACCAACGCCAGCCTGCTGGTGCGTGATGATTTTGCTTTCGAAGATGGTCTGTTCAGCGGCTACGACGCTGaaaa                                                                                       >  1:242177/1‑139 (MQ=255)

                          tGTCTGGCGTTTTGCGCTACCTGATCGAAAACAACAAAATCAACGCCGAATACGTTAAGCATTACACCAACGCCAGCCTGCTGGTGCGAGATGATTTTGCTTTCGAAGATGGt                                                                                                                 >  1:821640/1‑113 (MQ=255)

                                           tACCTGATCGAAAACAACAAAATCAACGCCGAATACGTTAAGCATTACACCAACGCCAGCCTGCTGGTGCGTGATGATTTTGCTTTCGAAGATGGTCTGTTCAGCGGCTACGACGCTGAAAAACGTCAATACGATAAAt                                                                      <  2:242177/139‑1 (MQ=255)

                                           tACCTGATCGAAAACAACAAAATCAACGCCGAATACGTTAAGCATTACACCAACGCCAGCCTGCTGGTGCGTGATGATTTTGCTTTCGAAGACGGTCTGTTCAGCGGCTACGACGCTGAAAAACGTCAATACGATAAAt                                                                      <  1:1278610/139‑1 (MQ=255)

                                             ccTGATCGAAAACAACAAAATCAACGCCGAATACGTTAAGCATTACACCAACGCCAGCCTGCTGGTGCGTGATGATTTTGCTTTCGAAGATGGTCTGTTCAGCGGCTACGACGCTGAAAAACGTCAATACGATaaa                                                                       >  1:383734/1‑136 (MQ=255)

                                             ccTGATCGAAAACAACAAAATCAACGCCGAATACGTTAAGCATTACACCAACGCCAGCCTGCTGGTGCGTGATGATTTTGCTTTCGAAGATGGTCTGTTCAGCGGCTACGACGCTGAAAAACGTCAATACGATaaa                                                                       <  2:383734/136‑1 (MQ=255)

                                                  tCGAAAACAACAAAATCAACGCCGAATACGTTAAGCATTACACCAACGCCAGCCTGCTGGTGCGTGATGATTTTGCTTTCGAAGATGGTCTGTTCAGCGGCTACGACGCTGAAAAACGTCa                                                                                 <  1:134884/121‑1 (MQ=255)

                                                  tCGAAAACAACAAAATCAACGCCGAATACGTTAAGCATTACACCAACGCCAGCCTGCTGGTGCGTGATGATTTTGCTTTCGAAGATGGTCTGTTCAGCGGCTACGACGCTGAAAAACGTCa                                                                                 >  2:134884/1‑121 (MQ=255)

                                                             aaaaTCAACGCCGAATACGTTAAGCATTACACCAACGCCAGCCTGCTGGTGCGTGATGATTTTGCTTTCGAAGATGGTCTGTTCAGCGGCTACGACGCTGAAAAACGTCAATACGATAAATCGTCCTGGAACTATCAGc                                                    <  2:1278513/139‑1 (MQ=255)

                                                                                        tACACCAACGCCAGCCTGCTGGTGCGTGATGATTTTGCTTTCGAAGATGGTCTGTTCa                                                                                                          >  1:21405/1‑58 (MQ=255)

                                                                                        tACACCAACGCCAGCCTGCTGGTGCGTGATGATTTTGCTTTCGAAGATGGTCTGTTCa                                                                                                          <  2:21405/58‑1 (MQ=255)

                                                                                        tACACCAACGCCAGCCTGCTGGTGCGTGATGATTTTGCTTTCGAAGATGGTCTGTTCAGCGGCTACGACGCTGAAAAACGTGAATACGATAAATCGTCCTGGAACTATCAGCTCGATGAAAACGGCTATGCGAAAcgcg                         >  2:765684/1‑139 (MQ=255)

                                                                                         acacCAACGCCAGCCTGCTGGTGCGTGATGATTTTGCTTTCGAAGATGGTCTGTTCAGCGGCTACGACGCTGAAAAACGTCAATACGATAAATCGTCCTGGAACTATCAGCTCGATGAAAACGGCTATGCGAAACACGa                        >  1:834019/1‑139 (MQ=255)

                                                                                               aCGCCAGCCTGCTGGTGCGTGATGATTTTGCTTTCGAAGATGGTCTGTTCAGCGGCTACGACGCTGAAAAACGTCAATACGATAAATCGTCCTGGAACTATCAGCTCGATGAAAACGGCTATGCGAAACGCGATGAAac                  >  1:561219/1‑139 (MQ=255)

                                                                                                  ccAGCCTGCTGGTGCGTGATGATTTTGCTTTCGAAGATGGTCTGTTCAGCGGCTACGACGCTGAAAAACGTCAATACGATAAATCGTCCTGGAACTATCAGCTCGAt                                               <  2:434907/107‑1 (MQ=255)

                                                                                                  ccAGCCTGCTGGTGCGTGATGATTTTGCTTTCGAAGATGGTCTGTTCAGCGGCTACGACGCTGAAAAACGTCAATACGATAAATCGTCCTGGAACTATCAGCTCGAt                                               >  1:434907/1‑107 (MQ=255)

                                                                                                      ccTGCTGGTGCGTGATGATTTTGCTTTCGAAGATGGTCTGTTCAGCGGCTACGACGCTGAAAAACGTCAATACGATAAATCGTc                                                                  <  2:701537/84‑1 (MQ=255)

                                                                                                      ccTGCTGGTGCGTGATGATTTTGCTTTCGAAGATGGTCTGTTCAGCGGCTACGACGCTGAAAAACGTCAATACGATAAATCGTc                                                                  >  1:701537/1‑84 (MQ=255)

                                                                                                             gTGCGTGATGATTTTGCTTTCGAAGATGGTCTGTTCAGCGGCTACGACGCTGaaa                                                                                        >  2:593950/1‑55 (MQ=255)

                                                                                                             gTGCGTGATGATTTTGCTTTCGAAGATGGTCTGTTCAGCGGCTACGACGCTGaaa                                                                                        <  1:593950/55‑1 (MQ=255)

                                                                                                              tGCGTGATGATTTTGCTTTCGAAGATGGTCTGTTCAGCGGCTACGACGCTGAAAAACGTCAATACGATAAATCGTCCTGGAACTATCAGCTCGATGAAAACGGCTATGCGAAACGCGATGAAACACTGACTCATCcgcg   <  1:476662/139‑1 (MQ=255)

                                                                                                              tGCGTGATGATTGTGCTTTCGAAGATGGTCTGTTCAGCGGCTACGACGCTGAAAAACGTCAATACGATAAATCGTCCTGGAACTATCAGCTCGATGAAAACGGCTATGCGAAACGCGATGAAACACTGACTCATCcgcg   <  2:274667/139‑1 (MQ=255)

                                                                                                               gCGTGATGATTTTGCTTTCGAAGATGGTCTGTTCAGCGGCTACGACGCTGAAAAACGTCAATACGATAAATCGTCCTGGAACTATCAGCTCGATGAAAACGGCTATGCGAAACGCGATGAAACACTGACTCATCCgcgc  <  2:561219/139‑1 (MQ=255)

                                                                                                                cGTGATGATTTTGCTTTCGAAGATGGTCTGTTCAGCGGCTACGACGCTGAAAAACGTCAATACGATAAATCGTCCTGGAACTATCAGCTCGATGAAAACGGCTATGCGAAAcg                           <  1:1034507/113‑1 (MQ=255)

                                                                                                                cGTGATGATTTTGCTTTCGAAGATGGTCTGTTCAGCGGCTACGACGCTGAAAAACGTCAATACGATAAATCGTCCTGGAACTATCAGCTCGATGAAAACGGCTATGCGAAAcg                           >  2:1034507/1‑113 (MQ=255)

                                                                                                                  tgatgaTTTTGCTTTCGAAGATGGTCTGTTCAGCGGCTACGACGCTGAAAAACGTCa                                                                                 >  1:69675/1‑57 (MQ=255)

                                                                                                                  tgatgaTTTTGCTTTCGAAGATGGTCTGTTCAGCGGCTACGACGCTGAAAAACGTCa                                                                                 <  2:69675/57‑1 (MQ=255)

                                                                                                                                 cGAAGATGGTCTGTTCAGCGGCTACGACGCTGAAAAACGTCAATACGATAAATCGTCCTGGAACTATCAGCTCGATGAAAACGGCTATGCGAAACGCGATGAAACACTGa             >  1:981825/1‑110 (MQ=255)

                                                                                                                                 cGAAGATGGTCTGTTCAGCGGCTACGACGCTGAAAAACGTCAATACGATAAATCGTCCTGGAACTATCAGCTCGATGAAAACGGCTATGCGAAACGCGATGAAACACTGa             <  2:981825/110‑1 (MQ=255)

                                                                                                                                  gAAGATGGTCTGTTCAGCGGCTACGACGCTGAAAAACGTCAATACGATAAATCGTCCTGGAACTATCAGCt                                                   <  1:573319/71‑1 (MQ=255)

                                                                                                                                  gAAGATGGTCTGTTCAGCGGCTACGACGCTGAAAAACGTCAATACGATAAATCGTCCTGGAACTATCAGCt                                                   >  2:573319/1‑71 (MQ=255)

TCGTTCCGGTACGGACATTACGTTCCTGTCTGGCGTTTTGCGCTACCTGATCGAAAACAACAAAATCAACGCCGAATACGTTAAGCATTACACCAACGCCAGCCTGCTGGTGCGTGATGATTTTGCTTTCGAAGACGGTCTGTTCAGCGGCTACGACGCTGAAAAACGTCAATACGATAAATCGTCCTGGAACTATCAGCTCGATGAAAACGGCTATGCGAAACGCGATGAAACACTGACTCATCCGCGC  >  NC_000913/1548225‑1548474

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A