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
A5 F1 I1 R1	81	47.9	2225048	94.8%	2109345	113.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,842,591	T→C	L151L (TTA→TTG)	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	2,842,591	0	T	C	100.0%	154.8 / NA	40	L151L (TTA→TTG)	hycI	protease involved in processing C‑terminal end of HycE
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (25/15); total (25/15)

ATGTCGCACGAACCATGAAGGCCCGATAAGCGCAGCGCATCGGGCAATTTAGCATTTGGCATCAGAGCTGGTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAACTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCGGGTAGTAAAAGCCGACGATATCCGGCTGAATGCCGAGGAAAATCACT  >  NC_000913/2842457‑2842723

aTGTCGCACGAACCATGAAGGCCCGATAAGCGCAGCGCATCGGGCAATTTAGCATTTGGCATCAGAGCTGGTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAACTACTCTTCTTCCACCGCCAACt                                                                                                                                  >  1:1075147/1‑139 (MQ=255)

    cGCACGAACCATGAAGGCCCGATAAGCGCAGCGCATCGGGCAATTTAGCACTTGGCATCAGAGCTGGTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAACTACTCTTCTTCCACCGCCAACTgcgc                                                                                                                              >  1:111901/1‑139 (MQ=255)

                     cacGATAAGCGCAGCGCATCGGGCAATTTAGCATTTGGCATCAGAGCTGGTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAGCCGCCATttcctt                                                                                                             >  1:666713/3‑139 (MQ=255)

                                   cgcaTCGGGCAATTTAGCATTTGGCATCAGAGCTGGTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGt                                                                                               >  2:389938/1‑139 (MQ=255)

                                            cAATTTAGCATTTGGCATCAGAGCTGGTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATaa                                                                                      <  1:344286/139‑1 (MQ=255)

                                             aaTTTAGCATTTGGCATCAGAGCTGGTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATaaa                                                                                     <  2:58668/139‑1 (MQ=255)

                                                         ggCATCAGAGCTGGTTCACCCCATTAAGAACATCCCTGTCCTGATTCCTTAATGAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCg                                                                         >  2:576958/1‑139 (MQ=255)

                                                                    tGGTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATc                                                              >  2:281239/1‑139 (MQ=255)

                                                                     ggTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCg                                                             >  1:535672/1‑139 (MQ=255)

                                                                         cACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTg                                                         <  2:883366/139‑1 (MQ=255)

                                                                         cACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTg                                                         <  1:281239/139‑1 (MQ=255)

                                                                                tCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATc                                                  >  2:215036/1‑139 (MQ=255)

                                                                                      aCATCCCTGTCCTGATTCCTTAATGAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCGGgtag                                            >  2:918011/1‑139 (MQ=255)

                                                                                         tCCCTGTCCTGATTCCTTAATGAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAGCCGCCAtt                                                                                                                  <  2:717543/66‑1 (MQ=255)

                                                                                         tCCCTGTCCTGATTCCTTAATGAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAGCCGCCAtt                                                                                                                  >  1:717543/1‑66 (MQ=255)

                                                                                          cccTGTCCTGATTCCTTAATGAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAgccgc                                                                                                                      <  1:1003075/61‑1 (MQ=255)

                                                                                          cccTGTCCTGATTCCTTAATGAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAgccgc                                                                                                                      >  2:1003075/1‑61 (MQ=255)

                                                                                          cccTGTCCTGATTCCTTAATGAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCGGGTAGTaaa                                        >  2:423567/1‑139 (MQ=255)

                                                                                          cccTGTCCTGATTCCTTAATGAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCGGGTAGTaaa                                        >  2:986618/1‑139 (MQ=255)

                                                                                              gTCCTGATTCCTTAATGAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCGGGTAGTAAAAGcc                                    >  1:1011541/1‑139 (MQ=255)

                                                                                               tCCTGATTCCTTAATGAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCGGGTAGTAAAAGCcg                                   >  2:444415/1‑139 (MQ=255)

                                                                                                    aTTCCTTAATGAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAGCCGCCATttccttcc                                                                                                           >  1:630097/1‑62 (MQ=255)

                                                                                                    aTTCCTTAATGAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAGCCGCCATttccttcc                                                                                                           <  2:630097/62‑1 (MQ=255)

                                                                                                    aTTCCTTAATGAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCg                                                                                             >  1:316150/1‑76 (MQ=255)

                                                                                                    aTTCCTTAATGAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCg                                                                                             <  2:316150/76‑1 (MQ=255)

                                                                                                    aTTCCTTAATGAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTAcc                                                                          >  2:43163/1‑95 (MQ=255)

                                                                                                    aTTCCTTAATGAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTAcc                                                                          <  1:43163/95‑1 (MQ=255)

                                                                                                    aTTCCTTAATGAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTAcc                                                                          <  2:649551/95‑1 (MQ=255)

                                                                                                    aTTCCTTAATGAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCGTCCAGTCGTTGATAAACGGTTTCTAcc                                                                          >  1:649551/1‑95 (MQ=255)

                                                                                                              gAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGc                                                           <  2:502499/100‑1 (MQ=255)

                                                                                                              gAAAAACTACTCTTCTTCCACCGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGc                                                           >  1:502499/1‑100 (MQ=255)

                                                                                                                   actactCTTCTTCCACCGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCAt                                                   <  1:2332/103‑1 (MQ=255)

                                                                                                                   actactCTTCTTCCACCGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCAt                                                   >  2:2332/1‑103 (MQ=255)

                                                                                                                       ctctTCTTCCACCGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCGGGTAGTAAAAGCCGACGATATCCGGCTGAATGCCGAgg           >  1:1072452/1‑139 (MQ=255)

                                                                                                                               ccACCGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCGGGTAGTAAAAGCCGACGATATCCGGCTGAATGCCGAGGAAAATCAc   >  1:846859/1‑139 (MQ=255)

                                                                                                                               ccACCGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCGGGTAGTAAAAGCCGACGATATCCGGCTGAATGCCGAGGAAAATCAc   >  2:807192/1‑139 (MQ=255)

                                                                                                                                cACCGCCAACTGCGCGAAGCCGCCATTTTCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCGGGTAGTAAAAGCCGACGATATCCGGCTGAATGCCGAGGAAAATCACt  <  2:666713/139‑1 (MQ=255)

                                                                                                                                cACCGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCGGGTAGTAAAAGCCGACGATATCCGGCTGAATGCCGAGGAAAATCACt  <  2:1075147/139‑1 (MQ=255)

                                                                                                                                  ccGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGt                                                                                 >  1:131513/1‑58 (MQ=255)

                                                                                                                                  ccGCCAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGt                                                                                 <  2:131513/58‑1 (MQ=255)

ATGTCGCACGAACCATGAAGGCCCGATAAGCGCAGCGCATCGGGCAATTTAGCATTTGGCATCAGAGCTGGTTCACCCCATCAAGAACATCCCTGTCCTGATTCCTTAATGAAAAACTACTCTTCTTCCACCGCTAACTGCGCGAAGCCGCCATTTCCTTCCCAGCCTTCCAGTCGTTGATAAACGGTTTCTACCGCATCTTTAATCGGCTGGGTCATCGGGTAGTAAAAGCCGACGATATCCGGCTGAATGCCGAGGAAAATCACT  >  NC_000913/2842457‑2842723

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 28 ≤` `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