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
A9 F1 I2 R1	760	52.7	2744488	90.2%	2475528	105.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,842,573	C→T	157 (TAG→TAA)	hycI ←	protease involved in processing C‑terminal end of HycE

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,842,573	0	C	T	100.0%	118.2 / NA	37	157 (TAG→TAA)	hycI	protease involved in processing C‑terminal end of HycE
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (21/16); total (21/16)

ATCCGGCCTACATGTCGCACGAACCATGAAGGCCCGATAAGCGCAGCGCATCGGGCAATTTAGCATTTGGCATCAGAGCTGGTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAACTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCGGGTAGTAAAAGCCGACGAT  >  NC_000913/2842446‑2842695

aTCCGGCCTACATGTCGCACGAACCATGAAGGCCCGATAAGCGCAGCGCATCGGGCAATTTAGCATTTGGCATCAGAGCTGGTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAATTACTCttcttc                                                                                                                 >  2:373154/1‑139 (MQ=255)

           aTGTCGCACGAACCATGAAGGCCCGATAAGCGCAGCGCATCGGGCAATTTAGCATTTGGCATCAGAGCTGGTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAATTACTCttcttc                                                                                                                 >  2:182373/1‑128 (MQ=255)

           aTGTCGCACGAACCATGAAGGCCCGATAAGCGCAGCGCATCGGGCAATTTAGCATTTGGCATCAGAGCTGGTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAATTACTCttcttc                                                                                                                 <  1:182373/128‑1 (MQ=255)

                     aaCCATGAAGGCCCGATAAGCGCAGCGCATCGGGCAATTTAGCATTTGGCATCAGAGCTGGTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAgcc                                                                                            >  1:122691/1‑139 (MQ=255)

                      aCCATGAAGGCCCGATAAGCGCAGCGCATCGGGCAATTTAGCATTTGGCATCAGAGCTGGTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAgccg                                                                                           >  1:197196/1‑139 (MQ=255)

                                cccGATAAGCGCAGCGCATCGGGCAATTTAGCATTTGGCATCAGAGCTGGTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATttcctt                                                                                 >  2:258822/1‑139 (MQ=255)

                                cccGATAAGCGCAGCGCATCGGGCAATTTAGCATTTGGCATCAGAGCTGGTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCAATttcctt                                                                                 >  1:830911/1‑139 (MQ=255)

                                  cGATAAGCGCAGCGCATCGGGCAATTTAGCATTTGGCATCAGAGCTGGTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATttccttcc                                                                               <  2:197196/139‑1 (MQ=255)

                                              cgcaTCGGGCAATTTAGCATTTGGCATCAGAGCTGGTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGt                                                                   <  2:122691/139‑1 (MQ=255)

                                                        aaTTTAGCATTTGGCATCAGAGCTGGTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATaaa                                                         <  2:703992/139‑1 (MQ=255)

                                                            tAGCATTTGGCATCAGAGCTGGTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAGTTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGACGTTGATAAACGGt                                                     <  2:830911/139‑1 (MQ=255)

                                                                    ggCATCAGAGCTGGTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCg                                             >  1:736549/1‑139 (MQ=255)

                                                                                ggTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAATTACTCTTCTTcc                                                                                                                >  1:1312630/1‑60 (MQ=255)

                                                                                ggTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAATTACTCTTCTTcc                                                                                                                <  2:1312630/60‑1 (MQ=255)

                                                                                    cACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTg                             <  1:373154/139‑1 (MQ=255)

                                                                                       cccATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCgg                                >  1:1155106/1‑133 (MQ=255)

                                                                                       cccATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCgg                                <  2:1155106/133‑1 (MQ=255)

                                                                                                     cccTGTCCTGATTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCg                                                                 <  1:1258439/86‑1 (MQ=255)

                                                                                                     cccTGTCCTGATTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCg                                                                 >  2:1258439/1‑86 (MQ=255)

                                                                                                         gTCCTGATTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAgccgc                                                                                          >  2:879796/1‑57 (MQ=255)

                                                                                                         gTCCTGATTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAgccgc                                                                                          <  1:879796/57‑1 (MQ=255)

                                                                                                         gTCCTGATTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCg                     >  1:1239549/1‑126 (MQ=255)

                                                                                                         gTCCTGATTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCg                     <  2:1239549/126‑1 (MQ=255)

                                                                                                            cTGATTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCGGGTAGTAAAAGCcgac     >  2:397877/1‑139 (MQ=255)

                                                                                                               aTTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTTCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCAt                       <  1:758938/118‑1 (MQ=255)

                                                                                                               aTTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTTCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCAt                       >  2:758938/1‑118 (MQ=255)

                                                                                                               aTTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATaa                                                          <  1:705379/83‑1 (MQ=255)

                                                                                                               aTTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATaa                                                          >  2:705379/1‑83 (MQ=255)

                                                                                                               aTTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCa                        <  1:521008/117‑1 (MQ=255)

                                                                                                               aTTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCa                        >  2:521008/1‑117 (MQ=255)

                                                                                                               aTTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCggg                   <  1:571729/122‑1 (MQ=255)

                                                                                                               aTTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCggg                   >  2:571729/1‑122 (MQ=255)

                                                                                                               aTTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCGGGTAGTAAAAGCCGACGat  >  2:441478/1‑139 (MQ=255)

                                                                                                               aTTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCGGGTAGTAAAAGCCGACGat  >  1:42948/1‑139 (MQ=255)

                                                                                                               aTTCCTTAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCGGGTAGTAAAAGCCGACGat  >  2:1183883/1‑139 (MQ=255)

                                                                                                                    ttAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATttcctt                                                                                 <  1:441492/55‑1 (MQ=255)

                                                                                                                    ttAATGAAAAATTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATttcctt                                                                                 >  2:441492/1‑55 (MQ=255)

ATCCGGCCTACATGTCGCACGAACCATGAAGGCCCGATAAGCGCAGCGCATCGGGCAATTTAGCATTTGGCATCAGAGCTGGTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAACTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCGGGTAGTAAAAGCCGACGAT  >  NC_000913/2842446‑2842695

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A