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
A1 F1 I2 R1	765	46.1	2269152	93.8%	2128464	105.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
JC	NC_000913	4,475,562	(G)_6→9	coding (126/1815 nt)	yjgL →	SopA‑central‑domain‑like hexapeptide repeat protein

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 4475556	0 (0.000)	48 (1.050) +GGG	30/192	0.3	100%	coding (120/1815 nt)	yjgL	SopA‑central‑domain‑like hexapeptide repeat protein
*	?	NC_000913	4475557 =	0 (0.000)	48 (1.050) +GGG	30/192	0.3	100%	coding (121/1815 nt)	yjgL	SopA‑central‑domain‑like hexapeptide repeat protein

TCAAGGAGTTCGTCATGAGCAAAATATCAGATTTAAATTATTCTCAACACATTACATTAGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGCC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/4475423‑4475556

‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTGGGTTATGTGGATTTTAGCAAACGCTCCAACGAAGCGGGTAGAAATATGATGGCT  >  NC_000913/4475557‑4475685

                                                                                                                                      ||||

TCAAGGAGTTCGTCATGAGCAAAATATCAGATTTAAATTATTCTCAACACATTACATTAGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGCC‑GGGGG                                                                                                                                 >  2:928407/1‑139

TCAAGGAGTTCGTCATGAGCAAAATATCAGATTTAAATTATTCTCAACACATTACATTAGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGCC‑GGGGG                                                                                                                                 >  1:315739/1‑139

TCAAGGAGTTCGTCATGAGCAAAATATCAGATTTAAATTATTCTCAACACATTACATTAGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGCC‑GGGG                                                                                                                                  >  2:248068/1‑138

TCAAGGAGTTCGTCATGAGCAAAATATCAGATTTAAATTATTCTCAACACATTACATTAGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGCC‑GGGG                                                                                                                                  <  1:248068/138‑1

    GGAGTTCGTCATGAGCAAAATATCAGATTTAAATTATTCTCAACACATTACATTAGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGCC‑GGGGGGGGG                                                                                                                             <  1:1014582/139‑1

                                       ATTCTCAACACATTACATTAGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGCC‑GGGGGGGGG                                                                                                                             >  2:279402/1‑104

                                       ATTCTCAACACATTACATTAGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGCC‑GGGGGGGGG                                                                                                                             <  1:279402/104‑1

                                                  ATTACATTAGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGCC‑GGGGGGGGGCAGGATAACAGAAGGAATATTCT                                                                                                      >  2:481571/1‑116

                                                  ATTACATTAGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGCC‑GGGGGGGGGCAGGATAACAGAAGGAATATTCT                                                                                                      <  1:481571/116‑1

                                                  ATTACATTAGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGCC‑GGGGGGGGGCAGGATAACAGA                                                                                                                 <  2:816295/105‑1

                                                  ATTACATTAGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGCC‑GGGGGGGGGCAGGATAACAGA                                                                                                                 >  1:816295/1‑105

                                                    TACATTGGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGCC‑GGGGGGGGG                                                                                                                             <  2:280440/91‑1

                                                    TACATTAGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGCC‑GGGTGGGGG                                                                                                                             >  1:280440/1‑91

                                                         TAGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGCC‑GGGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGC                                                                        >  2:474597/1‑139

                                                           GCCGACAATTTTAAACACAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATGGCC‑GGGGGGGGGCAGGATAACAGAAGGAATATTCT                                                                                                      >  2:650892/1‑107

                                                           GCCGACAATTTTAAACAAAAAAGTGAATTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGCC‑GGGGGGGGGCAGGATAACAGAAGGAATATTCT                                                                                                      <  1:650892/107‑1

                                                           GCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGCC‑GGGGGGGGG                                                                                                                             >  1:1015965/1‑84

                                                           GCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGCC‑GGGGGGGGG                                                                                                                             <  2:1015965/84‑1

                                                            CCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGCC‑GGGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAA                                                                     <  1:794714/139‑1

                                                                CAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGCC‑GGGGGGGGGCAGGCTAACAGAAGGAGTCTTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGAAAAGATA                                                                 >  2:237174/1‑139

                                                                CAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGCC‑GGGGGGGGG                                                                                                                             >  2:304966/1‑79

                                                                CAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGCC‑GGGGGGGGG                                                                                                                             <  1:304966/79‑1

                                                                 AATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGCC‑GGGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATAT                                                                <  1:237174/139‑1

                                                                      TAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGCC‑GGGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACC                                                           <  2:587498/139‑1

                                                                        AACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGCTTTTGGCCGTATTGGC‑GGGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTGTTGGCAAAGATATTTACCCT                                                         <  2:295319/139‑1

                                                                                         TTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGCC‑GGGG                                                                                                                                  <  1:627590/49‑1

                                                                                         TTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGCC‑GGGG                                                                                                                                  >  2:627590/1‑49

                                                                                                 CTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGCC‑GGGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTGGGTTATGTGGATTTTAGCAAA                                   <  1:782892/136‑1

                                                                                                 CTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGCC‑GGGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTGGGTTATGTGGATTTTAGCAAA                                   >  2:782892/1‑136

                                                                                                        GTTGGAATGAATGATTTTGCCCGTATTGCC‑GGGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTGGGTTATGTGGATTTTAGCAAA                                   >  2:972820/1‑129

                                                                                                        GTTGGAATGAATGATTTTGCCCGTATTGCC‑GGGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTGGGTTATGTGGATTTTAGCAAA                                   <  1:972820/129‑1

                                                                                                         TTGGAATGAATGATTTTGCCCGTATTGCC‑GGGGGGGGGCAGGATAACAGAAGGAATATT                                                                                                        <  2:438362/59‑1

                                                                                                         TTGGAATGAATGATTTTGCCCGTATTGCC‑GGGGGGGGGCAGGATAACAGAAGGAATATT                                                                                                        >  1:438362/1‑59

                                                                                                         TTGGAATGAATGATTTTGCCCGTATTGCC‑GGGGGGGGGCAGGATAACAGAAG                                                                                                               >  1:911839/1‑52

                                                                                                         TTGGAATGAATGATTTTGCCCGTATTGCC‑GGGGGGGGGCAGGATAACAGAAG                                                                                                               <  2:911839/52‑1

                                                                                                          TGGAATGAATGATTTTGCCCGTATTGCC‑GGGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTGGGTTATGTGGATTTTAGCAAACGCTCCAACGAA                       <  1:474597/139‑1

                                                                                                           GGAATGAATGATTTTGCCCGTATTGCC‑GGGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTCAGAGTTTTTGGCAAA                                                                     <  2:324727/92‑1

                                                                                                           GGAATGAATGATTTTGCCCGTATTGCC‑GGGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTCAGAGTTTTTGGCAAA                                                                     >  1:324727/1‑92

                                                                                                                 AATGATTTTGCCCGTATTGCCGGGGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACC                                                           >  2:285983/1‑97

                                                                                                                 AATGATTTTGCCCGTATTGCCGGGGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACC                                                           <  1:285983/97‑1

                                                                                                                 AATGATTTTGCCCGTATTGCC‑GGGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTGGGTTATGTGGATTTTAGCAAACGCTCCAACGAAGCGGGT                 <  1:407613/138‑1

                                                                                                                 AATGATTTTGCCCGTATTGCC‑GGGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTGGGTTATGTGGATTTTAGCAAACGCTCCAACGAAGCGGGT                 >  2:407613/1‑138

                                                                                                                   TGATTTTGCCCGTATTGCC‑GGGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCA                                                                       >  1:79513/1‑82

                                                                                                                   TGATTTTGCCCGTATTGCC‑GGGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCA                                                                       <  2:79513/82‑1

                                                                                                                         TGCCCGTATTGCC‑GGGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTGGGTTATGTGGATTTTAGCAAACGCTCCAACGAAGCGGGTAGAAATATG        <  1:928407/139‑1

                                                                                                                           CCCGTATTGCC‑GGGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTGGGTTATGTGGATTTTAGCAAACGCTCCAACGAAGCGGGTAGAAATATGAT      >  1:450830/1‑139

                                                                                                                           CCCGTATTGCC‑GGGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTGGGTTATGTGGATTTTAGCAAACGCTCCAACGAAGCGGGTAGAAATATGAT      <  2:450830/139‑1

                                                                                                                               TATTGCC‑GGGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTGGGTTATGTGGATTTTAGCAAACGCTCCAACGAAGCGGGTAGAAATATGATGGCT  <  1:220136/139‑1

                                                                                                                                ATTGCC‑‑GGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTGGGTTATGTGGATTTTAGCAAACGCTCCAACGAAGCGGGT                 <  1:451834/122‑1

                                                                                                                                ATTGCC‑‑GGGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTGGGTTATGTGGATTTTAGCAAACGCTCCAACGAAGCGGGT                 >  2:451834/1‑122

                                                                                                                                      ||||

TCAAGGAGTTCGTCATGAGCAAAATATCAGATTTAAATTATTCTCAACACATTACATTAGCCGACAATTTTAAACAAAAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGCC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/4475423‑4475556

‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTGGGTTATGTGGATTTTAGCAAACGCTCCAACGAAGCGGGTAGAAATATGATGGCT  >  NC_000913/4475557‑4475685

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `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