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	4,110,806	A→G	G234G (GGT→GGC)	tpiA ←	triosephosphate isomerase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,110,806	0	A	G	93.5%	95.4 / ‑2.1	31	G234G (GGT→GGC)	tpiA	triosephosphate isomerase
Reads supporting (aligned to +/- strand): ref base A (1/1); new base G (13/16); total (14/17)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.37e-01

TGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGCCTGTTTAGCCGCTTCTGCAGCTTTAACGATTACTGCGAAGGCGTCAGCTTTCAGAGAAGCACCACCAACCAGCGCGCCGTCGATATCCGGCTGAGCAAACAGTTCTGCAGCGTTAGACGCGTTTACAGAGCCGCCGTACTGAATGATCACTTGTTCAGCGATGTTAGCGTCAACTTTAGCGATGTGGTCACGG  >  NC_000913/4110670‑4110938

tgAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGCCTGTTTAGCCGCTTCTGCAGCTTTAACGATTACTGCGAAGGCGTCAGCTTTCAGAGAAGcgcc                                                                                                                                    >  1:409528/1‑139 (MQ=255)

          cGTTAAGGCGAAGCGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTAAAGCCTGTTTAGCCGCTTCTGCAGCTTTAACGATTACTGCGAAGGCGTCAGCTTTCAGAGAAGCGCCACCAACCAgc                                                                                                                          >  1:339480/1‑139 (MQ=255)

                 gCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGCCTGTTTAGCCGCTTCTGCAGCTTTAACGATTACTGCGAAGGCGTCAGCTTTCAGAGAAGCGCCACCAACCAGCGCGCCGt                                                                                                                   <  2:409528/139‑1 (MQ=255)

                                  gtaagtGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGCCTGTTTAGCCGCTTCTGCAGCTTTAACGATTACTGCGAAGGCGTCAGCTTTCAGAGAAGCGCCACCAACCAGCGCGCCGTCGATATCCGGCTGAGCa                                                                                                  >  2:389478/1‑139 (MQ=255)

                                     agtGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGCCTGTTTAGCCGCTTCTGCAGCTTTAACGATTACTGCGAAGGCGTCAGCTTTCAGAGAAGCGCCACCAACCAGCGCGCCGTCGATATCCGGCTGAGCAAAc                                                                                               >  1:581211/1‑139 (MQ=255)

                                        gCCGGATATGAAATCCGGCACCTGTCAGACTTAAGCCTGTTTAGCCGCTTCTGCAGCTTTAACGATTACTGCGAAGGCGTCAGCTTTCAGAGAAGCGCCACCAACCAGCGCGCCGTCGATATCCGGCTGAGCAAACAGt                                                                                            >  2:478852/1‑139 (MQ=255)

                                                      ccGGCACCTGTCAGACTTAAGCCTGTTTAGCCGCTTCTGCAGCTTTAACGATTACTGCGAAGGCGTCAGCTTTCAGAGAAGCGCCACCAACCAGCGCGCCGTCGATATCCGGCTGAGCAAACAGTTCAGCAGCGTTCGa                                                                              <  1:466110/139‑1 (MQ=255)

                                                                   gACTTAAGCCTGTTTAGCCGCTTCTGCAGCTTTAACGATTACTGCGAAGGCGTCAGCTTTCAGAGAAGCGCCACCAACCAGCGCGCCGTCGATATCCGGCTGAGCAAACAGTTCTGCAGCGTTAGACGCGTTTACagag                                                                 <  2:358109/139‑1 (MQ=255)

                                                                     cTTAAGCCTGTTTAGCCGCTTCTGCAGCTTTAACGATTACTGCGAAGGCGTCAGCTTTCAGAGAAGCGCCACCAACCAGCGCGCCGTCGATATCCGGCTGAGCAAACAGTTCTGCAGCGTTAGACGCGTTTACAGAgcc                                                               >  1:687933/1‑139 (MQ=255)

                                                                              gTTTAGCCGCTTCTGCAGCTTTAACGATTACTGCGAAGGCGTCAGCTTTCAGAGAAGCGCCACCAACCAGCGCGCCGTCGATATCCGGCTGAGCAAACAGTTCTGCAGCGTTAGACGCGTTTACAGAGCCGCCGTACTg                                                      >  1:699599/1‑139 (MQ=255)

                                                                                ttAGCCGCTTCTGCAGCTTTAACGATTACTGCGAAGGCGTCAGCTTTCAGAGAAGCGCCACCAACCAGCGCGCCGTCGATATCCGGCTGAGCAAACAGTTCTGCAGCGTTAGACGCGTTTACAGAGCCGCCGTACTGaa                                                    <  2:765435/139‑1 (MQ=255)

                                                                                    ccGCTTCTGCAGCTTTAACGATTACTGCGAAGGCGTCAGCTTTCAGAGAAGCGCCACCAACCAGCGCGCCGt                                                                                                                   <  2:91246/72‑1 (MQ=255)

                                                                                    ccGCTTCTGCAGCTTTAACGATTACTGCGAAGGCGTCAGCTTTCAGAGAAGCGCCACCAACCAGCGCGCCGt                                                                                                                   >  1:91246/1‑72 (MQ=255)

                                                                                            gCAGCTTTAACGATTACTGCGAAGGCGTCAGCTTTCAGAGAAGCGCCACCAACCAGCGCGCCGTCGATATCCGGCTGAGCAAACAGTTCTGCAGCGTTAGACGCGTTTACAGAGCCGCCGTACTGAATGATCACTTGtt                                        <  2:692660/139‑1 (MQ=255)

                                                                                               gCTTTAACGATTACTGCGAAGGCGTCAGCTTTCAGAGAAGCGCCACCAACCAGCGCGCCGTCGATATCCGGCTGAGCAAACAGTTCTGCAGCGTTAGACGCGTTTACAGAGCCGCCGTACTGAATGATCACTTGTTCAg                                     <  1:426591/139‑1 (MQ=255)

                                                                                                    aaCGATTACTGCGAAGGCGTCAGCTTTCAGAGAAGCGCCACCAACCAGCGCGCCGTCGATATCCGGCTGAGCAAACAGTTCTGCAGCGTTAGAcgcg                                                                          <  1:405784/97‑1 (MQ=255)

                                                                                                    aaCGATTACTGCGAAGGCGTCAGCTTTCAGAGAAGCGCCACCAACCAGCGCGCCGTCGATATCCGGCTGAGCAAACAGTTCTGCAGCGTTAGAcgcg                                                                          >  2:405784/1‑97 (MQ=255)

                                                                                                     aCGATTACTGCGAAGGCGTCAGCTTTCAGAGAAGCGCCACCAACCAGCGCGCCGTCGATATCCGGCTGAGCAAACAGTTCTGCAGCGTTAGACGCGTTTACAGAGCCGCCGTACTGAATGATCACTTGTTCAg                                     <  1:687863/133‑1 (MQ=255)

                                                                                                     aCGATTACTGCGAAGGCGTCAGCTTTCAGAGAAGCGCCACCAACCAGCGCGCCGTCGATATCCGGCTGAGCAAACAGTTCTGCAGCGTTAGACGCGTTTACAGAGCCGCCGTACTGAATGATCACTTGTTCAg                                     >  2:687863/1‑133 (MQ=255)

                                                                                                          tACTGCGAAGGCGTCAGCTTTCAGAGAAGCGCCACCAACCAGCGCGCCGTCGATATCCGGCTGAGCAAACAGTTCTGCAGCGTTAGACGCGTTTACAGAGCCGCCGTACTGAATGATCACTTGTTCAGCGATGTTAGCg                          <  2:335461/139‑1 (MQ=255)

                                                                                                          tACTGCGAAGGCGTCAGCTTTCAGAGAAGCGCCACCAACCAGCGCGCCGTCGATATCCGGCTGAGCAAACAGTTCTGCAGCGTTAGACGCGTTTACAGAGCCGCCGTACTGAATGATCACTTGTTCAGCGATGTTAGCg                          >  1:335461/1‑139 (MQ=255)

                                                                                                           aCTGCGAAGGCGTCAGCTTTCAGAGAAGCGCCACCAACCAGCGCGCCGTCGATATCCGGCTGAGCAAACAGTTCTGCAGCGTTAGACGCGTTTACAGAGCCGCCGTACTGAATGATCACTTGTTCAGCGATGTTAGCGt                         <  2:581211/139‑1 (MQ=255)

                                                                                                            cTGCGAAGGCGTCAGCTTTCAGAGAAGCGCCACCAACCAGCGCGCCGTCGATATCCGGCTGAGCAAACAGTTCTGCAGCGTTAGACGCGTTTACAGAGCCGCCGTACTGAATGATCACTTGTTCAGCGATGTTAGCGTc                        <  2:159830/139‑1 (MQ=255)

                                                                                                              gCGAAGGCGTCAGCTTTCAGAGAAGCGCCACCAACCAGCGCGCCGTCGATATCCGGCTGAGCAAACAGTTCTGCAGCGTTAGACGCGTTTACAGAGCCGCCGTACTGAATGATCACTTGTTCAGCGATGTTAGCGTCaa                      <  2:95258/139‑1 (MQ=255)

                                                                                                                 aaGGCGTCAGCTTTCAGAGAAGCGCCACCAACCAGCGCGCCGTCGATATCCGGCTGAGCAAACAGTTCTGCAGCGTTAGACGCGTTTACAGAgccg                                                              <  2:163169/96‑1 (MQ=255)

                                                                                                                 aaGGCGTCAGCTTTCAGAGAAGCGCCACCAACCAGCGCGCCGTCGATATCCGGCTGAGCAAACAGTTCTGCAGCGTTAGACGCGTTTACAGAgccg                                                              >  1:163169/1‑96 (MQ=255)

                                                                                                                       tCAGCTTTCAGAGAAGCACCACCAACCAGCGCGCCGTCGATATCCGGCTGAGCAAACAGTTCTGCAGCGTTAGACGCGTTTACAGAGCCGCCGTAc                                                        <  2:600274/96‑1 (MQ=255)

                                                                                                                       tCAGCTTTCAGAGAAGCACCACCAACCAGCGCGCCGTCGATATCCGGCTGAGCAAACAGTTCTGCAGCGTTAGACGCGTTTACAGAGCCGCCGTAc                                                        >  1:600274/1‑96 (MQ=255)

                                                                                                                         aGCTTTCAGAGAAGCGCCACCAACCAGCGCGCCGTCGATATCCGGCTGAGCAAACAGTTCTGCAGCGTTa                                                                                >  2:45606/1‑70 (MQ=255)

                                                                                                                         aGCTTTCAGAGAAGCGCCACCAACCAGCGCGCCGTCGATATCCGGCTGAGCAAACAGTTCTGCAGCGTTa                                                                                <  1:45606/70‑1 (MQ=255)

                                                                                                                              tCAGAGAAGCGCCACCAACCAGCGCGCCGTCGATATCCGGCTGAGCAAACAGTTCTGCAGCGTTAGACGCGTTTACAGAGCCGCCGTACTGAATGATCACTTGTTCAGCGATGTTAGCGTCAACTTTAGCGATGTGGTc      >  1:208847/1‑139 (MQ=255)

                                                                                                                                  agaAGCGCCACCAACCAGCGCGCCGTCGATATCCGGCTGAGCAAACAGTTCTGCAGCGTTAGACGCGTTTACAGAGCCGCCGTACTGAATGATCACTTGTTCAGCGATGTTAGCGTCAACTTTAGCGATGTGGTCACgg  <  1:389478/139‑1 (MQ=255)

TGAGATTTTGCGTTAAGGCGAAGAGTTAAGGAAAGTAAGTGCCGGATATGAAATCCGGCACCTGTCAGACTTAAGCCTGTTTAGCCGCTTCTGCAGCTTTAACGATTACTGCGAAGGCGTCAGCTTTCAGAGAAGCACCACCAACCAGCGCGCCGTCGATATCCGGCTGAGCAAACAGTTCTGCAGCGTTAGACGCGTTTACAGAGCCGCCGTACTGAATGATCACTTGTTCAGCGATGTTAGCGTCAACTTTAGCGATGTGGTCACGG  >  NC_000913/4110670‑4110938

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A