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
A139 F1 I1 R1	15	48.9	3081653	97.3%	2998448	76.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
JC JC	REL606	1,886,669	IS1 (–) +9 bp	intergenic (‑499/+162)	yobF ← / ← yebO	hypothetical protein/hypothetical protein

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	REL606	1886669 =	9 (0.210)	91 (1.870)	64/150	0.0	89.9%	intergenic (‑499/+170)	yobF/yebO	hypothetical protein/hypothetical protein
*	?	REL606	= 2035093	NA (NA)	91 (1.870)	64/150	0.0	89.9%	noncoding (1/768 nt)	IS1	repeat region
*	?	REL606	= 1886677	9 (0.210)	60 (1.240)	45/150	0.1	85.4%	intergenic (‑507/+162)	yobF/yebO	hypothetical protein/hypothetical protein
*	?	REL606	= 1974039	NA (NA)	60 (1.240)	45/150	0.1	85.4%	noncoding (768/768 nt)	IS1	repeat region

CTGGTCTGACTTCAAATAATTATCATATTATTTATTTGCGTAACGGGATATCAGAAAAAGATATTTTCCTCATT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  REL606/1886742‑1886669

‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAG  <  REL606/2035093‑2035019

CTGGTCTGACTTCAAATAATTATCATATTATTTATTTGCGTAACGGGATATCAGAAAAAGATATTTTCCTCATTGc                                                                           <  1:805409/76‑2

CTGGTCTGACTTCAAATAATTATCATATTATTTATTTGCGTAACGGGATATCAGAAAAAGATATTTTCCTCATTGG                                                                           <  2:1517398/76‑1

CTGGTCTGACTTCAAATAATTATCATATTATTTATTTGCGTAACGGGATATCAGAAAAAGATATTTTCCTCATTGG                                                                           >  1:1418538/1‑76

 TGGTCTGACTTCAAATAATTATCATATTATTTATTTGCGTAACGGGATATCAGAAAAAGATATTTTCCTCATTGGT                                                                          >  1:1089725/1‑76

  GGTCTGACTTCAAATAATTATCATATTATTTATTTGTGTAACGGGATATCAGAAAAAGATATTTTCCTCATTGGTG                                                                         >  1:446446/1‑76

  GGTCTGACTTCAAATAATTATCATATTATTTATTTGCGTAACGGGATATCAGAAAAAGATATTTTCCTCATTGGTG                                                                         <  2:519533/76‑1

  GGTCTGACTTCAAATAATTATCATATTATTTATTTGCGTAACGGGATATCAGAAAAAGATATTTTCCTCATTGGTG                                                                         >  1:938728/1‑76

     CTGACTTCAAATAATTATCATATTATTTATTTGCGTAACGGGATATCAGAAAAAGATATTTTCCTCATTGGTGATG                                                                      >  1:967862/1‑76

      TGACTTCAAATAATTATCATATTATTTATTTGCGTAACGGGATATCAGAAAAAGATATTTTCCTCATTGGTGATGC                                                                     >  1:507264/1‑76

       GACTTCAAATAATCATCATATTATTTATTTGCGTAACGGGATATCAGAAAAAGATATTTTCCTCATTGGTGATGCT                                                                    >  1:1020527/1‑76

        ACTTCAAATAATTATCATATTATTTATTTGCGTAACGGGATATCAGAAAAAGATATTTTCCTCATTGGTGATGCTG                                                                   <  1:829594/76‑1

         CTTCAAATAATTATCATATTATTTATTTGCGTAACGGGATATCAGAAAAAGATATTTTCCTCATTGGTGATGCTGC                                                                  <  1:606566/76‑1

          TTCAAATAATTATCATATTATTTATTTGCGTAACGGGATATCAGAAAAAGATATTTTCCTCATTGGTGATGCTGCC                                                                 >  2:1334649/1‑76

           cCAAATAATTATCATATTATTTATTTGCGTAACGGGATATCAGAAAAAGATATTTTCCTCATTGGTGATGCTGCCA                                                                >  1:806366/2‑76

           TCAAATAATTATCATATTATTTATTTGCGTAACGGGATATCAGAAAAAGATATTTTCCTCATTGGTGATGCTGCCA                                                                <  1:774045/76‑1

            CAAATAATTATCATATTATTTATTTGCGTAACGGGATATCAGAAAAAGATATTTTCCTCATTGGTGATGCTGCCAn                                                               <  1:205051/76‑2

            CAAATAATTATCATATTATTTATTTGCGTAACGGGATATCAGAAAAAGATATTTTCCTCATTGGTGATGCTGCCAA                                                               >  2:906383/1‑76

             AAATAATTATCATATTATTTATTTGCGTAACGGGAGATCAGAAAAAGATATTTTCCTCATTGGTGATGCTGCCAAC                                                              >  2:1372205/1‑76

              AATAATTATCATATTATTTATTTGCGTAACGGGATATCAGAAAAAGATATTTTCCTCATTGGTGATGCTGCCAACT                                                             <  1:26934/76‑1

              AATAATTATCATATTATTTATTTGCGTAACGGGATATCAGAAAAAGATATTTTCCTCATTGGTGATGCTGCCAACT                                                             <  1:1406692/76‑1

              AATAATTATCATATTATTTATTTGCGTAACGGGATATCAGAAAAAGATATTTTCCTCATTGGTGATGCTGCCAACT                                                             >  1:999901/1‑76

               ATAATTATCATATTATTTATTTGCGTAACGGGATATCAGAAAAAGATATTTTCCTCATTGGTGATGCTGCCAACTT                                                            <  2:1490441/76‑1

                  ATTATCATATTATTTATTTGCGTAACGGGATATCAGAAAAAGATATTTTCCTCATTGGTGATGCTGCCAACTTACT                                                         <  2:1327853/76‑1

                   TTATCATATTATTTATTTGCGTAACGGGATATCAGAAAAAGATATTTTCCTCATTGGTGATGCTGCCAACTTACTG                                                        >  2:471281/1‑76

                   TTATCATATTATTTATTTGCGTAACGGGATATCAGAAAAAGATATTTTCCTCATTGGTGATGCTGCCAACTTACTG                                                        >  2:357938/1‑76

                    TATCATATTATTTATTTGCGTAACGGGATATCAGAAAAAGATATTTTCCTCATTGGTGATGCTGCCAACTTACTGA                                                       <  2:1027334/76‑1

                     ATCATATTATTTATTTGCGTAACGGGATATCAGAAAAAGATATTTTCCTCATTGGTGATGCTGCCAACTTACTGAT                                                      >  1:541869/1‑76

                      TCATATTATTTATTTGCGTAACGGGATATCAGAAAAAGATATTTTCCTCATTGGTGATGCTGCCAACTTACTGATT                                                     >  2:753059/1‑76

                      TCATATTATGTATTTGCGTAACGGGATATCAGAAAAAGATATTTTCCTCATTGGTGATTCTGCCAACTTACTGATT                                                     <  2:406518/76‑1

                       CATAGTATTTATTTGCGTAACGGGATATCAGGAAAAGATATTTTCCTCATTAGTGATGCTGCCAACTTACTGATTT                                                    <  2:679056/76‑1

                          ATTATTTATTTGCGTAACGGGATATCAGAAAAAGATATTTTCCTCATTGGTGATGCTGCCAACTTACTGATTTAGT                                                 <  1:1100879/76‑1

                           TTATTTATTTGCGTAACGGGATATCAGAAAAAGATATTTTCCTCATTGGTGATGCTGCCAACTTACTGATTTAGTG                                                <  2:1356664/76‑1

                            TATTTATTTGCGTAACGGGATATCAGAAAAAGATATTTTCCTCATTGGTGATGCTGCCAACTTACTGATTTAGTGT                                               >  1:428516/1‑76

                            TATTTATTTGCGTAACGGGATATCAGAAAAAGATATTTTCCTCATTGGTGATGCTGCCAACTTACTGATTTAGTGT                                               >  1:90680/1‑76

                            TATTTATTTGCGTAACGGGATATCAGAAAAAGATATTTTCCTCATTGGTGATGCTGCCAACTTACTGATTTAGTGT                                               <  1:801951/76‑1

                             ATTTATTTGCGTAACGGGATATCAGAAAAAGATATTTTCCTCATTGGTGATGCTGCCAACTTACTGATTTAGTGTA                                              <  2:889177/76‑1

                               TTATTTGCGTAACGGGATATCAGAAAAAGATATTTTCCTCATTGGTGATGCTGCCAACTTACTGATTTAGTGTATG                                            <  2:720049/76‑1

                                TATTTGCGTAACGGGATATCAGAAAAAGATATTTTCCTCATTGGTGATGCTGCCAACTTACTGATTTAGTGTATGA                                           >  2:144042/1‑76

                                TATTTGCGTAACGGGATATCAGAAAAAGATATTTTCCTCATTGGTGATGCTGCCAACTTACTGATTTAGTGTATGA                                           <  2:1509692/76‑1

                                  TTTGCGTAGCGGGATATCAGAAAAAGATATTTTCCTCATTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATG                                         <  2:1242557/76‑1

                                  TTTGCGTAACGGGATATCAGAAAAAGATATTTTCCTCATTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATG                                         <  1:1501477/76‑1

                                      CGTAACGGGATATCAGAAAAAGATATTTTCCTCATTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGT                                     >  1:383808/1‑76

                                       GTAACGGGATATCAGAAAAAGATATTTTCCTCATTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTT                                    >  2:273422/1‑76

                                        TAACGGGATATCAGAAAAAGATATTTTCCTCATTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTT                                   >  2:783614/1‑76

                                        TAACGGGATATCAGAAAAAGATATTTTCCTCATTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTT                                   >  1:31821/1‑76

                                        TAACGGGATATCAGAAAAAGATATTTTCCTCATTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTT                                   <  2:989854/76‑1

                                          ACGGGATATCAGAAAAAGATATTTTCCTCATTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTT                                 >  2:949274/1‑76

                                           CGGGATATCAGAAAAAGATATTTTCCTCATTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTG                                >  1:108942/1‑76

                                           CGGGATATCAGAAAAAGATATTTTCCTCATTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTG                                >  2:712076/1‑76

                                             GGATATCAGAAAAAGATATTTTCCTCATTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAG                              >  2:274713/1‑76

                                              GATATCAGAAAAAGATATTTTCCTCATTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGG                             >  1:1320780/1‑76

                                               ATATCAGAAAAAGATATTTTCCTCATTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGT                            >  1:1280766/1‑76

                                               ATATCAGAAAAAGATATTTTCCTCATTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGT                            <  2:1115833/76‑1

                                               ATATCAGAAAAAGATATTTTCCTCATTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGT                            >  2:352886/1‑76

                                               ATATCAGAAAAAGATATTTTCCTCATTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTATGAGGT                            >  1:732480/1‑76

                                                TATCAGAAAAAGATATTTTCCTCATTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTG                           <  2:167172/76‑1

                                                TATCAGAAAAAGATATTTTCCTCATTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTG                           >  2:396344/1‑76

                                                 ATCAGAAAAAGATATTTTCCTCATTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGCGGTGC                          >  2:1516985/1‑76

                                                   CAGAAAAAGATATTTTCCTCATTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTC                        >  1:1176039/1‑76

                                                     GAAAAAGATATTTTCCTCATTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCA                      >  2:610934/1‑76

                                                     GAAAAAGATATTTTCCTCATTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCA                      <  2:43987/76‑1

                                                     GAAAAAGATATTTTCCTCATTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCA                      <  2:1069514/76‑1

                                                     GAAAAAGATATTTTCCTCATTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCA                      <  2:201707/76‑1

                                                     GAAAAAGATATTTTCCTCATTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCA                      <  2:1296514/76‑1

                                                      AAAAAGATATTTTCCTCATTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAG                     <  2:1115952/76‑1

                                                      AAAAAGATATTTTCCTCATTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAG                     <  2:151845/76‑1

                                                       AAAAGATATTTTCCTCATTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGT                    <  2:1308765/76‑1

                                                        AAAGATATTTTCCTCATTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTG                   <  1:1090963/76‑1

                                                        AAAGATATTTTCCTCATTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTG                   >  2:420603/1‑76

                                                          AGATATTTTCCTCATTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGC                 >  1:1252263/1‑76

                                                             TATTTTCCTCATTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTC              >  1:1334702/1‑76

                                                             TATTTTCCTCATTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTC              <  1:911469/76‑1

                                                              ATTTTCCTCATTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCT             >  1:712317/1‑76

                                                              ATTTTCCGCATTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCT             >  1:567379/1‑76

                                                               TTTTCCTCATTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTG            >  2:1460049/1‑76

                                                                  TCCTCATTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTT         >  2:1318598/1‑76

                                                                  TCCTCATTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTT         >  2:577839/1‑76

                                                                    CTCATTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCT       >  2:223539/1‑76

                                                                    CTCATTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCT       <  2:1068312/76‑1

                                                                     TCATTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTA      >  2:297339/1‑76

                                                                      tATTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTAT     <  2:148054/75‑1

                                                                      CATTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTAc     >  2:1305534/1‑75

                                                                      CATTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTAT     >  1:854752/1‑76

                                                                      CATTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTAT     <  2:148066/76‑1

                                                                        TTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCA   <  1:1475856/76‑1

                                                                        TTGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCA   >  1:1293841/1‑76

                                                                        TTGGAGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGCGCTCCAGTGGCTTCTGTTTCTATCA   >  1:1523489/1‑76

                                                                         TGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTTTATCAG  >  2:624428/1‑76

                                                                         TGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAG  >  1:980202/1‑76

                                                                         TGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAG  <  1:809141/76‑1

                                                                         TGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAG  <  2:993719/76‑1

CTGGTCTGACTTCAAATAATTATCATATTATTTATTTGCGTAACGGGATATCAGAAAAAGATATTTTCCTCATT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  REL606/1886742‑1886669

‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAG  <  REL606/2035093‑2035019

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 24 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`
Reads not counted as support for junction
read_name Not counted due to insufficient overlap past the breakpoint.
read_name Not counted due to not crossing MOB target site duplication.

GATK/CNVnator alignment

N/A