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
A10 F1 I2 R1	757	38.1	1607544	96.5%	1551279	117.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,250,629	(C)_5→6	coding (210/1071 nt)	dhaK ←	dihydroxyacetone kinase, PTS‑dependent, dihydroxyacetone‑binding subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,250,624	1	.	C	92.9%	80.3 / ‑2.0	28	A72G (GCC→GGC)	dhaK	dihydroxyacetone kinase, PTS‑dependent, dihydroxyacetone‑binding subunit
Reads supporting (aligned to +/- strand): ref base . (0/0); major base C (12/14); minor base T (1/1); total (13/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.41e-01

TCGCTGTTTCAAAGTTAAGAATATCGCCGGTGTAATTTTTGATAATCAACAGTACACCTTCGCCGCCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGG‑CCCCCGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTGCCGCCACCCGACAGCAGGGCGACTTTTCCTGCAACAGGGGCATCAGCTCGGGTGACATACACCG  >  NC_000913/1250490‑1250744

tCGCTGTTTCAAAGTTAAGAATATCGCCGGTGTAATTTTTGATAATCAACAGTACACCTTCGCCGCCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGG‑cccc                                                                                                                      >  2:298897/1‑139 (MQ=255)

    tGTTTCAAAGTTAAGAATATCGCCGGTGTAATTTTTGATAATCAACAGTACACCTTCGCCGCCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGG‑ccccccga                                                                                                                  <  1:570475/139‑4 (MQ=255)

              ttAAGAATATCGCCGGTGTAATTTTTGATAATCAACAGTACACCTTCGCCGCCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCCCGAAAGCATcccc                                                                                                         >  1:234921/1‑139 (MQ=255)

                  gAATATCGCCGGTGTAATTTTTGATAATCAACAGTACACCTTCGCCGCCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCCCGAAAGCATCCCCTGAc                                                                                                     <  1:298897/139‑1 (MQ=255)

                  gAATATCGCCGGTGTAATTTTTGATAATCAACAGTACACCTTCGCCGCCATCAACTTGCATGGCGAATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCCCGAAAGCATCCCCTGAc                                                                                                     <  1:128649/139‑1 (MQ=255)

                   aaTATCGCCGGTGTAATTTTTGATAATCAACAGTACACCTTCGCCGCCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCCCGAAAGCATCCCCTGAcc                                                                                                    <  1:403053/139‑1 (MQ=255)

                                        gATAATCAACAGTACACCTTCGCCGCCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCCCGAAAGCATCCCCTGACCGATATAACCACAGTGCATCgg                                                                               >  1:61760/1‑139 (MQ=255)

                                               aaCAGTACACCTTCGCCGCCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCCCGAAAGCATCCCCTGACCGATATAAc                                                                                            >  1:167200/1‑119 (MQ=255)

                                               aaCAGTACACCTTCGCCGCCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCCCGAAAGCATCCCCTGACCGATATAAc                                                                                            <  2:167200/119‑1 (MQ=255)

                                                         cTTCGCCGCCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCCCGAAAGCATCCCCTGa                                                                                                      >  1:239090/1‑99 (MQ=255)

                                                         cTTCGCCGCCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCCCGAAAGCATCCCCTGa                                                                                                      <  2:239090/99‑1 (MQ=255)

                                                            cgccgcCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCCCGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTGCCGCCAc                                                           >  1:515103/1‑139 (MQ=255)

                                                              ccgccATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCCCGAAAGCATCCCCTGa                                                                                                      <  1:264901/94‑1 (MQ=255)

                                                              ccgccATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCCCGAAAGCATCCCCTGa                                                                                                      >  2:264901/1‑94 (MQ=255)

                                                                       aCTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCCCGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTGCCGCCACCCGACAGCAgg                                                <  2:225209/139‑1 (MQ=255)

                                                                           gCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCCCGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTGCCGCCACCCGACAGCAGGGCGa                                            >  2:765814/1‑139 (MQ=255)

                                                                            cATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCCCGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTGCCGCCACCCGACAGCAGGGCGAc                                           >  1:153368/1‑139 (MQ=255)

                                                                              tGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAATTTTCGCCCGGACAGGCCCCCCGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGc                                                                              >  2:579313/1‑102 (MQ=255)

                                                                              tGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAATTTTCGCCCGGACAGGCCCCCCGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGc                                                                              <  1:579313/102‑1 (MQ=255)

                                                                              tGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGTCCCCCGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGc                                                                              <  1:797293/102‑1 (MQ=255)

                                                                              tGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGTCCCCCGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGc                                                                              >  2:797293/1‑102 (MQ=255)

                                                                              tGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCCCGAAAGc                                                                                                               >  1:335352/1‑69 (MQ=255)

                                                                              tGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCCCGAAAGc                                                                                                               <  2:335352/69‑1 (MQ=255)

                                                                                     ttCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCCCGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTGCCGCCACCCGACAGCAGGGCGACTTTTCCTGc                                  >  2:141273/1‑139 (MQ=255)

                                                                                                    gggCGTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCCCGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTGCCGCCACCCGACAGCAGGGCGACTTTTCCTGCAACAGGGGCATCAGc                   <  1:141273/139‑1 (MQ=255)

                                                                                                        gTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCCCGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTGCCGCCACCCGACAGCAGGGCGACTTTTCCTGCAACAGGGGCATCAGCTCgg               <  2:515103/139‑1 (MQ=255)

                                                                                                        gTCGGTGAGGTGAAAATTTCGCCCGGACAGGCCCCCCGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTGCCGCCACCCGACAGCAGGGCGACTTTTCCTGCAACAGGGGCATCAGCTCgg               >  2:604967/1‑139 (MQ=255)

                                                                                                                     aaaTTTCGCCCGGACAGGCCCCCCGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTGCCGCCACCCGACAGCAGGGCGACTTTTCCTGCAACAGGGGCATCAGCTCGGGTGACATACACCg  <  2:153368/139‑1 (MQ=255)

                                                                                                                     aaaTTTCGCCCGGACAGGCCCCCCGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTGCCGCCACCCGACAGCAGGGCGACTTTTCCTGCAACAGGGGCATCAGCTCGGGTGACATACACCg  <  1:765814/139‑1 (MQ=255)

                                                                                                                     aaaTTTCGCCCGGACAGGCCCCCCGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTGCCGCCACCCGACAGCAGGGCGACTTTTCCTGCAACAGGGGCATCAGCTCGGGTGACATACACCg  <  1:190032/139‑1 (MQ=255)

TCGCTGTTTCAAAGTTAAGAATATCGCCGGTGTAATTTTTGATAATCAACAGTACACCTTCGCCGCCATCAACTTGCATGGCGCATTCAAAGATTTTATCGGGCGTCGGTGAGGTGAAAATTTCGCCCGGACAGG‑CCCCCGAAAGCATCCCCTGACCGATATAACCACAGTGCATCGGCTCGTGTCCGCTGCCGCCACCCGACAGCAGGGCGACTTTTCCTGCAACAGGGGCATCAGCTCGGGTGACATACACCG  >  NC_000913/1250490‑1250744

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