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
A7 F1 I2 R1	766	64.2	3232166	90.9%	2938038	104.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,712,518	(C)_6→7	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	100.0%	176.4 / NA	51	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 . (0/0); new base C (26/25); total (26/25)

GTTAAAATCATTTAAATTTACACACGCAACAAATATTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGATTATTACAAAGGACTT  >  NC_000913/1712381‑1712639

gTTAAAATCATTTAAATTTACACACGCAACAAATATTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑ccccccc                                                                                                                          <  1:1378391/139‑2 (MQ=255)

        cATTTAAATTTACACACGCAACAAATATTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTcagtg                                                                                                                   <  1:864591/139‑1 (MQ=255)

          tttAAATTTACACACGCAACAAATATTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTcagtgca                                                                                                                 >  2:869960/1‑139 (MQ=255)

                                     gACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGtttttt                                                                                      >  1:1102834/1‑139 (MQ=255)

                                          aCAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGaaaa                                                                                 >  2:1517493/1‑139 (MQ=255)

                                           cAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACCAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGaaaaa                                                                                >  1:1137785/1‑139 (MQ=255)

                                                  ttACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACg                                                                         <  2:300336/139‑1 (MQ=255)

                                                  ttACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACg                                                                         >  1:685267/1‑139 (MQ=255)

                                                     cacTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCa                                                                                                                                  >  2:641095/1‑79 (MQ=255)

                                                     cacTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCa                                                                                                                                  <  1:641095/79‑1 (MQ=255)

                                                     cacTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTg                                                                      >  2:1374706/1‑139 (MQ=255)

                                                          gCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATaa                                                                 >  2:1595388/1‑139 (MQ=255)

                                                                      aaaCTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCGGGaa                                                     <  2:1102834/139‑1 (MQ=255)

                                                                                   tcACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTccc                                        <  1:1517493/139‑1 (MQ=255)

                                                                                    cACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTcccc                                       >  2:800893/1‑139 (MQ=255)

                                                                                      cTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGc                                     <  1:1595388/139‑1 (MQ=255)

                                                                                      cTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGc                                     <  1:800893/139‑1 (MQ=255)

                                                                                      cTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGCTTTTTGAAAAATTTAACTCTGGATAACATTCCACGAAATGGTTGAATTCCCCGc                                     >  1:513329/1‑139 (MQ=255)

                                                                                       tAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGcc                                    <  1:621760/139‑1 (MQ=255)

                                                                                       tAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGcc                                    <  2:522095/139‑1 (MQ=255)

                                                                                        aGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCt                                   <  2:1381708/139‑1 (MQ=255)

                                                                                        aGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCCCTCCGTGCAGTGAAAAAATCTGCCGGTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGCAATGGTTGAATTCCCCGCCt                                   <  2:513329/139‑1 (MQ=255)

                                                                                         gTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTc                                  >  2:522477/1‑139 (MQ=255)

                                                                                           aaaaaCGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACg                                                                         >  1:418175/1‑98 (MQ=255)

                                                                                           aaaaaCGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACg                                                                         <  2:418175/98‑1 (MQ=255)

                                                                                           aaaaaCGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCt                                   >  1:633302/1‑136 (MQ=255)

                                                                                           aaaaaCGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCt                                   <  2:633302/136‑1 (MQ=255)

                                                                                           aaaaaCGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAg                                <  2:1550639/139‑1 (MQ=255)

                                                                                           aaaaaCGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAAAGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAg                                >  1:1550639/1‑139 (MQ=255)

                                                                                            aaaaCGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGaa                                                                                   <  1:372486/87‑1 (MQ=255)

                                                                                            aaaaCGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGaa                                                                                   >  2:372486/1‑87 (MQ=255)

                                                                                             aaaCGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGtt                              >  1:671597/1‑139 (MQ=255)

                                                                                               aCGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTtat                            <  2:682456/139‑1 (MQ=255)

                                                                                               aCGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTtat                            <  2:1137785/139‑1 (MQ=255)

                                                                                               aCGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTtat                            >  2:767800/1‑139 (MQ=255)

                                                                                                 gCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACg                                                                         <  1:631953/92‑1 (MQ=255)

                                                                                                 gCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACg                                                                         >  2:631953/1‑92 (MQ=255)

                                                                                                   tAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGt                        >  1:230829/1‑139 (MQ=255)

                                                                                                     aaTAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTaa                      <  1:767800/139‑1 (MQ=255)

                                                                                                            gAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGatta               <  2:685267/139‑1 (MQ=255)

                                                                                                            gAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGatta               <  1:522477/139‑1 (MQ=255)

                                                                                                             aaCATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGGATTCCCCGCCTCAGTTATATGTAACAGattat              >  1:216639/1‑139 (MQ=255)

                                                                                                                  atCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCt                                   >  2:621072/1‑113 (MQ=255)

                                                                                                                  atCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCt                                   <  1:621072/113‑1 (MQ=255)

                                                                                                                  atCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTtata                           <  2:170510/121‑1 (MQ=255)

                                                                                                                  atCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTtata                           >  1:170510/1‑121 (MQ=255)

                                                                                                                  atCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGATTATTACaa         >  1:793424/1‑139 (MQ=255)

                                                                                                                    cGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTaa                      <  2:1210276/124‑1 (MQ=255)

                                                                                                                    cGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTaa                      >  1:1210276/1‑124 (MQ=255)

                                                                                                                     gCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGGATTCCCCGCCTCAGTTATATGTAACAGATTATTACAAAgg      <  2:216639/139‑1 (MQ=255)

                                                                                                                       cGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCt                                   <  2:623596/108‑1 (MQ=255)

                                                                                                                       cGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCt                                   >  1:623596/1‑108 (MQ=255)

                                                                                                                         ttAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGATTATTACAAAGGACtt  >  1:593120/1‑139 (MQ=255)

                                                                                                                         ttAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGATTATTACAAAGGACtt  >  1:575615/1‑139 (MQ=255)

GTTAAAATCATTTAAATTTACACACGCAACAAATATTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGATTATTACAAAGGACTT  >  NC_000913/1712381‑1712639

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A