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 I2 R1	762	35.5	1545288	95.5%	1475750	117.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,712,518	(C)_6→8	intergenic (+360/‑251)	nth → / → dtpA	DNA glycosylase and apyrimidinic (AP) lyase (endonuclease III)/dipeptide and tripeptide permease A

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,712,512	1	.	C	97.5%	133.9 / ‑3.4	40	intergenic (+354/‑257)	nth/dtpA	DNA glycosylase and apyrimidinic (AP) lyase (endonuclease III)/dipeptide and tripeptide permease A
Reads supporting (aligned to +/- strand): ref base . (0/1); new base C (22/17); total (22/18)
Fisher's exact test for biased strand distribution p-value = 4.50e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.68e-01
*	NC_000913	1,712,512	2	.	C	97.5%	137.4 / ‑3.4	40	intergenic (+354/‑257)	nth/dtpA	DNA glycosylase and apyrimidinic (AP) lyase (endonuclease III)/dipeptide and tripeptide permease A
Reads supporting (aligned to +/- strand): ref base . (0/1); new base C (22/17); total (22/18)
Fisher's exact test for biased strand distribution p-value = 4.50e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.68e-01

AGGTTAAAATCATTTAAATTTACACACGCAACAAATATTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑‑CCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAA  >  NC_000913/1712379‑1712619

||

aGGTTAAAATCATTTAAATTTACACACGCAACAAATATTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑‑ccccc                                                                                                        >  1:335621/1‑139 (MQ=255)

 ggTTAAAATCATTTAAATTTACACACGCAACAAATATTGACGTACAAAACATTACACTGGCTATTATTCAGAAACTAGACTATCTCACTAGAAAAACCGCGAAATAACAGAGCATATCGCCGTTAAGCCATcc‑‑cccccc                                                                                                       <  2:576024/139‑1 (MQ=255)

      aaaTCATTTAAATTTACACACGCAACAAATATTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑‑CCCCCCcctct                                                                                                  <  2:747843/139‑2 (MQ=255)

            tttAAATTTACACACGCAACAAATATTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCCTCTcagtgc                                                                                              >  1:227211/1‑139 (MQ=255)

            tttAAATTTACACACGCAACAAATATTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCCTCTcagtgc                                                                                              >  2:132790/1‑139 (MQ=255)

                 aTTTACACACGCAACAAATATTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCCTCTCAGTGCAGTGa                                                                                         >  1:445344/1‑139 (MQ=255)

                                       gACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGttttt                                                                   >  2:89655/1‑139 (MQ=255)

                                       gACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGttttt                                                                   >  2:268507/1‑139 (MQ=255)

                                                     tACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACg                                                     <  2:335621/139‑1 (MQ=255)

                                                       cacTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCt                                                   >  1:381848/1‑139 (MQ=255)

                                                          tGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCCTCTCAGTGTAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGa                                                >  1:222585/1‑139 (MQ=255)

                                                            gCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCCTCTcagtgc                                                                                              >  1:509471/1‑91 (MQ=255)

                                                            gCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCCTCTcagtgc                                                                                              <  2:509471/91‑1 (MQ=255)

                                                            gCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCCTCTCAGTGCAGTGAAAAAAt                                                                                   >  2:756509/1‑102 (MQ=255)

                                                            gCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCCTCTCAGTGCAGTGAAAAAAt                                                                                   <  1:756509/102‑1 (MQ=255)

                                                            gCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATa                                              >  1:662748/1‑139 (MQ=255)

                                                            gCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATa                                              >  2:601069/1‑139 (MQ=255)

                                                             cTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATaa                                             >  1:211868/1‑139 (MQ=255)

                                                                      aGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑‑c                                                                                                            <  1:67255/65‑1 (MQ=255)

                                                                      aGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑‑c                                                                                                            >  2:67255/1‑65 (MQ=255)

                                                                        aaaCTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGa                                  >  1:58808/1‑139 (MQ=255)

                                                                         aaCTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGaa                                 <  1:601069/139‑1 (MQ=255)

                                                                                    ctcACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTc                      >  1:278531/1‑139 (MQ=255)

                                                                                      cACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGaa                                 >  1:532639/1‑126 (MQ=255)

                                                                                      cACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGaa                                 <  2:532639/126‑1 (MQ=255)

                                                                                      cACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTccc                    <  2:278531/139‑1 (MQ=255)

                                                                                        cTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCg                  >  1:252805/1‑139 (MQ=255)

                                                                                        cTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCg                  >  1:450255/1‑139 (MQ=255)

                                                                                          aGTAAAAACGCTAAATAGCAGAACATATCGCCTTTAAGCCATCACCCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGGTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGcc                <  2:381848/139‑1 (MQ=255)

                                                                                           gTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCt               <  2:450255/139‑1 (MQ=255)

                                                                                           gTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCt               <  2:58808/139‑1 (MQ=255)

                                                                                           gTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCt               <  1:83393/139‑1 (MQ=255)

                                                                                             aaaaaCGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCt               <  2:139684/137‑1 (MQ=255)

                                                                                             aaaaaCGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCt               >  1:139684/1‑137 (MQ=255)

                                                                                              aaaaCGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTccc                    <  2:625926/131‑1 (MQ=255)

                                                                                              aaaaCGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTccc                    >  1:625926/1‑131 (MQ=255)

                                                                                              aaaaCGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAg            <  1:563826/139‑1 (MQ=255)

                                                                                              aaaaCGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAg            <  1:89655/139‑1 (MQ=255)

                                                                                              aaaaCGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAg            <  2:636525/139‑1 (MQ=255)

                                                                                                aaCGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGtt          <  1:730156/139‑1 (MQ=255)

                                                                                                 aCGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTta         >  1:77371/1‑139 (MQ=255)

                                                                                                   gCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTtata       >  1:653991/1‑139 (MQ=255)

                                                                                                       aaTAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTa   >  2:266582/1‑139 (MQ=255)

                                                                                                        aTAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTaa  <  1:583475/139‑1 (MQ=255)

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AGGTTAAAATCATTTAAATTTACACACGCAACAAATATTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑‑CCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAA  >  NC_000913/1712379‑1712619

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