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
A13 F1 I1 R1	86	24.1	1002126	98.1%	983085	121.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,007,295	T→C	V345A (GTG→GCG)	ygeW →	putative carbamoyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,007,295	0	T	C	92.9%	89.1 / ‑1.3	28	V345A (GTG→GCG)	ygeW	putative carbamoyltransferase
Reads supporting (aligned to +/- strand): ref base T (1/1); new base C (13/13); total (14/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.78e-01

CGCAACACAAAGACTGGCATTGTACTGAAGAGATGATGGAACTGACCCGTGATGGCGAAGCCCTGTACATGCACTGCCTGCCAGCTGATATCAGCGGCGTATCCTGTAAAGAAGGTGAAGTGACTGAAGGCGTATTCGAAAAATACCGTATCGCTACCTACAAAGAAGCCAGCTGGAAGCCTTATATCATCGCCGCGATGATCCTGTCCCGTAAATACGCCAAACCAGGTGCACTGCTCGAGCAACTGCTGAAAG  >  NC_000913/3007175‑3007429

cgcAACACAAAGACTGGCATTGTACTGAAGAGATGATGGAACTGACCCGTGATGGCGAAGCCCTGTACATGCACTGCCTGCCAGCTGATATCAGCGGCGTATCCTGTAAAGAAGGTGAAGCGACTGAAGGCGTATTCGa                                                                                                                      >  2:361089/1‑139 (MQ=255)

             cTGGCATTGTACTGAAGAGATGATGGAACTGACCCGTGATGGCGAAGCCCTGTACATGCACTGCCTGCCAGCTGATATCAGCGGCGTATCCTGTAAAGAAGGTGAAGCGACTGAAGGCGTATTCGAAAAATACCGTATc                                                                                                         >  1:154840/1‑139 (MQ=255)

             cTGGCATTGTACTGAAGAGATGATGGAACTGACCCGTGATGGCGAAGCCCTGTACATGCACTGCCTGCCAGCTGATATCAGCGGCGTATCCTGTAAAGAAGGTGAAGCGACTGAAGGCGTATTCGAAAAATACCGTATc                                                                                                         <  2:129257/139‑1 (MQ=255)

                                atgatgGAACTGACCCGTGATGGCGAAGCCCTGTACATGCACTGCCTGCCAGCTGATATCAGCGGCGTATCCTGTAAAGAAGGTGAAGCGACTGAAGGc                                                                                                                              <  1:129967/99‑1 (MQ=255)

                                atgatgGAACTGACCCGTGATGGCGAAGCCCTGTACATGCACTGCCTGCCAGCTGATATCAGCGGCGTATCCTGTAAAGAAGGTGAAGCGACTGAAGGc                                                                                                                              >  2:129967/1‑99 (MQ=255)

                                  gatgGAACTGACCCGTGATGACGAAGCCCTGTACATGCACTGCCTGCCAGCTGATATCAGCGGCGTATCCTGTAAAGAAGGTGAAGCGACTGAAGGCGTATTCGAAAAATACCGTATCGCTAGCTACAAAGAAGCCAGc                                                                                    >  2:339425/1‑139 (MQ=255)

                                      gAACTGACCCGTGATGGCGAAGCCCTGTACATGCACTGCCTGCCAGCTGATATCAGCGGCGTATCCTGTAAAGAAGGTGAAGCGACTGAAGGCGTATTCGAAAAATACCGTATCGCTACCTACAAAGAAGCCAGCTGGa                                                                                <  2:214453/139‑1 (MQ=255)

                                        aCTGACCCGTGATGGCGAAGCCCTGTACATGCACTGCCTGCCAGCTGATATCAGCGGCGTATCCTGTAAAGAAGGTGAAGCGACTGAAGGCGTATTCGAAAAATACCGTATCGCTACCTACAAAGAAGCCAGCTGGAAg                                                                              <  2:154840/139‑1 (MQ=255)

                                                         aaGCCCTGTACATGCACTGCCTGCCAGCTGATATCAGCGGCGTATCCTGTAAAGAAGGTGAAGCGACTGAAGGCGTATTCGAAAAATACCGTATCGCTACCTACAAAGAAGCCAGCTGGAAGCCTTATATCATcgccgc                                                             >  1:394566/1‑139 (MQ=255)

                                                           gCCCTGTACATGCACTGCCTGCCAGCTGATATCAGCGGCGTATCCTGTAAAGAAGGTGAAGCGACTGAAGGCGTATTCGAAAAATACCGTATCGCTACCTACAAAGAAGCCAGCTGGAAGCCTTATATCATCGCCGCga                                                           <  1:361089/139‑1 (MQ=255)

                                                                         ctgcctgcCAGCTGATATCAGCGGCGTATCCTGTAAAGAAGGTGAAGCGACTGAAGGCGTATTCGAAAAATACCGTATCGCTACCTACAAAGAAGCCAGCTGGAAGCCTTATATCATCGCCGCGATGATCCTGTCCCGt                                             >  1:450557/1‑139 (MQ=255)

                                                                           gcctgccAGCTGATATCAGCGGCGTATCCTGTAAAGAAGGTGAAGTGACTGAAGGCGTATTCGAAAAATACCGTATCGct                                                                                                      >  1:455010/1‑80 (MQ=255)

                                                                           gcctgccAGCTGATATCAGCGGCGTATCCTGTAAAGAAGGTGAAGTGACTGAAGGCGTATTCGAAAAATACCGTATCGct                                                                                                      <  2:455010/80‑1 (MQ=255)

                                                                           gcctgccAGCTGATATCAGCGGCGTATCCTGTAAAGAAGGTGAAGCGACTGAAGGCGTATTCGAAAAATACCGTATCGCTACCTACAAAGAAGCCAGCTGGAAGCCTTATATCATCGCCGCGATGATCCTGTCCCGTaa                                           >  2:297162/1‑139 (MQ=255)

                                                                           gcctgccAGCTGATATCAGCGGCGTATCCTGTAAAGAAGGTGAAGCGACTGAAGGCGTATTCGAAAAATACCGTATCGCTACCTACAAAGAAGCCAGCTGGAAGCCTTATATCATCGCCGCGATGATCCTGTCCCGTaa                                           >  2:411180/1‑139 (MQ=255)

                                                                           gcctgccAGCTGATATCAGCGGCGTATCCTGTAAAGAAGGTGAAGCGACTGAAGGCGTATTCGAAAAATACCGTATCGCTACCTACAAAGAAGCCAGCTGGAAGCCTTATATCATCGCCGCGATGATCCTGTCCCGTaa                                           >  1:46923/1‑139 (MQ=255)

                                                                           gcctgccAGCTGATATCAGCGGCGTATCCTGTAAAGAAGGTGAAGCGACTG‑AGGCGTATTCGAAAAATACCGTATCGCTACCTACAAAGAAGCCAGCTGGa                                                                                <  2:381810/101‑1 (MQ=255)

                                                                           gcctgccAGCTGATATCAGCGGCGTATCCTGTAAAGAAGGTGAAGCGACTG‑AGGCGTATTCGAAAAATACCGTATCGCTACCTACAAAGAAGCCAGCTGGa                                                                                >  1:381810/1‑101 (MQ=255)

                                                                                    cTGATATCAGCGGCGTATCCTGTAAAGAAGGTGAAGCGACTGAAGGCGTATTCGAAAAATACCGTATCGCTACCTACAAAGAAGCCAGCTGGAAGCCTTATATCATCGCCGCGATGATCCTGTCCCGTAAATACGCCaa                                  <  2:450557/139‑1 (MQ=255)

                                                                                             gcggcgTATCCTGTAAAGAAGGTGAAGCGACTGAAGGCGTATTCGAAAAATACCGTATCGCTACCTACAAAGAAGCCAGCTGGAAGCCTTATATCATCGCCGCGATGATCCTGTCCCGTAAATACGCCAAACCAGGTGc                         <  2:277267/139‑1 (MQ=255)

                                                                                                   tATCCTGTAAAGAAGGTGAAGCGACTGAAGGCGTATTCGAAAAATACCGTATCGCTACCTACAAAGAAGCCAGCTGGAAGCCTTATATCATCGCCGCGATGATCCTGTCCCGTAAATACGCCAAACCAGGTGCACTGCt                   >  2:71174/1‑139 (MQ=255)

                                                                                                          tAAAGAAGGTGAAGCGACTGAAGGCGTATTCGAAAAATACCGTATCGCTACCTACAAAGAAGCCAGCTGGAAGCCTTATATCATCGCCGCGATGATCCTGTCCCGTAAATACGCCAAACCAGGTGCACTGCTCGAGCaa            <  2:283552/139‑1 (MQ=255)

                                                                                                               aagGTGAAGCGACTGAAGGCGTATTCGAAAAATACCGTATCGCTACCTACAAAGAAGCCAGCTGGAAGCCTTATATCATCGCCGCGATGATCCTGTCCCGTAAATACGCCAAACCAGGTGCACTGCTCGAGc              <  2:322598/132‑1 (MQ=255)

                                                                                                               aagGTGAAGCGACTGAAGGCGTATTCGAAAAATACCGTATCGCTACCTACAAAGAAGCCAGCTGGAAGCCTTATATCATCGCCGCGATGATCCTGTCCCGTAAATACGCCAAACCAGGTGCACTGCTCGAGCAActgct       >  2:370147/1‑139 (MQ=255)

                                                                                                               aagGTGAAGCGACTGAAGGCGTATTCGAAAAATACCGTATCGCTACCTACAAAGAAGCCAGCTGGAAGCCTTATATCATCGCCGCGATGATCCAGTCCCGTAAATACGCCAAACCAGGTGCACTGCTCGAGc              >  1:322598/1‑132 (MQ=255)

                                                                                                                    gAAGCGACTGAAGGCGTATTCGAAAAATACCGTATCGCTACCTACAAAGAAGCCAGCTGGAAGCCTTATATCATCGCCGCGATGATCCTGTCCCGTAAATACGCCAAACCAGGTGCACTGCTCGAGCAACTGCTGAaag  <  1:375771/139‑1 (MQ=255)

                                                                                                                    gAAGCGACTGAAGGCGTATTCGAAAAATACCGTATCGCTACCTACAAAGAAGCCAGCTGGAAGCCTTATATCATCGCCGCGATGATCCTGTCCCGTAAATACGCCAAACCAGGTGCACTGCTCGAGCAACTGCTGAaag  <  1:411180/139‑1 (MQ=255)

                                                                                                                    gAAGCGACTGAAGGCGTATTCGAAAAATACCGTATCGCTACCTACAAAGAAGCCAGCTGGAAGCCTTATATCATCGCCGCGATGATCCTGTCCCGTAAATACGCCAAACCAGGTGCACTGCTCGAGCAACTGCTGAaag  <  1:297162/139‑1 (MQ=255)

CGCAACACAAAGACTGGCATTGTACTGAAGAGATGATGGAACTGACCCGTGATGGCGAAGCCCTGTACATGCACTGCCTGCCAGCTGATATCAGCGGCGTATCCTGTAAAGAAGGTGAAGTGACTGAAGGCGTATTCGAAAAATACCGTATCGCTACCTACAAAGAAGCCAGCTGGAAGCCTTATATCATCGCCGCGATGATCCTGTCCCGTAAATACGCCAAACCAGGTGCACTGCTCGAGCAACTGCTGAAAG  >  NC_000913/3007175‑3007429

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A