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
A3 F1 I1 R1	781	46.9	2231650	93.5%	2086592	109.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	417,373	C→T	P78S (CCA→TCA)	phoB →	response regulator in two‑component regulatory system with PhoR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	417,373	0	C	T	100.0%	133.5 / NA	43	P78S (CCA→TCA)	phoB	response regulator in two‑component regulatory system with PhoR
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (26/17); total (26/17)

TGACAGTGCTGTGAATCAACTGAATGAACCCTGGCCGGATTTAATTCTCCTCGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTCCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCG  >  NC_000913/417246‑417503

tGACAGTGCTGTGAATCAACTGAATGAACCCTGGCCGGATTTAATTCTCCTCGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTAAGTGGTGATg                                                                                                                         >  2:174766/1‑139 (MQ=255)

     gTGCTGTGAATCAACTGAATGAACCCTGGGCGGATTTAATTCTCCTCGTCTGGAGGTTATTTGGCGGCTCAGGCACCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAATGGTTATGTTTAc                                                                                                                    >  2:156453/1‑139 (MQ=255)

           tgAATCAACTGAATGAACCCTGGCCGGATTTAATTCTCCTCGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCag                                                                                                              >  2:1064599/1‑139 (MQ=255)

            gAATCAACTGAATGAACCCTGGCCGGATTTAATTCTCCTCGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAgtg                                                                                                                               >  1:527644/1‑121 (MQ=255)

            gAATCAACTGAATGAACCCTGGCCGGATTTAATTCTCCTCGACAGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAgtg                                                                                                                               <  2:527644/121‑1 (MQ=255)

                cAACTGAATGAACCCTGGCCGGATTTAATTCTCCTCGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAgggg                                                                                                         <  2:687513/139‑1 (MQ=255)

                cAACTGAATGAACCCTGGCCGGAATTAATTCTCCTCGACTGGATTTTACCTTGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAgcgg                                                                                                         <  1:156453/139‑1 (MQ=255)

                  aCTGTATGAACCCTGGCCGGATTTATTTCTCCTCGACTGGATGTTACCTGGCGGCACCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGgaa                                                                                                       >  2:783552/1‑139 (MQ=255)

                  aCTGAATGAACCCTGGCCGGATTTAATTCTCCTCGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCag                                                                                                              <  1:53050/132‑1 (MQ=255)

                  aCTGAATGAACCCTGGCCGGATTTAATTCTCCTCGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCag                                                                                                              >  2:53050/1‑132 (MQ=255)

                             ccTGGCCGGATTTAATTCTCCTCGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGgaaga                                                                                                     <  2:180906/130‑1 (MQ=255)

                             ccTGGCCGGATTTAATTCTCCTCGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGgaaga                                                                                                     >  1:180906/1‑130 (MQ=255)

                             ccTGGCCGGATTTAATTCTCCTCGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATcg                                                                                            >  1:873420/1‑139 (MQ=255)

                                 gCCGGATTTAATTCTCCTCGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAgggg                                                                                                         >  2:661709/1‑122 (MQ=255)

                                 gCCGGATTTAATTCTCCTCGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAgggg                                                                                                         <  1:661709/122‑1 (MQ=255)

                                               tcctcGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAgggg                                                                                                         <  2:767606/108‑1 (MQ=255)

                                               tcctcGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAgggg                                                                                                         >  1:767606/1‑108 (MQ=255)

                                                 ctcGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAgggg                                                                                                         <  1:526770/106‑1 (MQ=255)

                                                 ctcGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAgggg                                                                                                         >  2:526770/1‑106 (MQ=255)

                                                 ctcGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCg                                                                        >  2:680449/1‑139 (MQ=255)

                                                 ctcGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCg                                                                        <  2:427209/139‑1 (MQ=255)

                                                  tcGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCgg                                                                       >  1:857196/1‑139 (MQ=255)

                                                    gACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGgcg                                                                     <  2:873420/139‑1 (MQ=255)

                                                      cTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGcgcg                                                                   <  1:680449/139‑1 (MQ=255)

                                                         gATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGcgcg                                                                   <  1:308514/136‑1 (MQ=255)

                                                         gATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGcgcg                                                                   >  2:308514/1‑136 (MQ=255)

                                                         gATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGAt                                                                >  1:39639/1‑139 (MQ=255)

                                                              tACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACta                                                           >  1:933649/1‑139 (MQ=255)

                                                                           cGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGgcg                                                                     >  1:176834/1‑116 (MQ=255)

                                                                           cGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGgcg                                                                     <  2:176834/116‑1 (MQ=255)

                                                                                     ttCATCAAACACCTCAAGTGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGa                                    >  1:555493/1‑139 (MQ=255)

                                                                                     ttCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGtt                                                                                                                       >  1:734090/1‑56 (MQ=255)

                                                                                     ttCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGtt                                                                                                                       <  2:734090/56‑1 (MQ=255)

                                                                                     ttCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGa                                    >  2:772392/1‑139 (MQ=255)

                                                                                     ttCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGAATGACTATATCACCAAGCCGTTTTCGCCGa                                    >  1:408243/1‑139 (MQ=255)

                                                                                                 cTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGgcg                                                                     >  1:817889/1‑94 (MQ=255)

                                                                                                 cTCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGgcg                                                                     <  2:817889/94‑1 (MQ=255)

                                                                                                  tCAAGCGCGAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGgc                       >  2:320275/1‑139 (MQ=255)

                                                                                                         cgAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCg                                                                        >  2:274024/1‑83 (MQ=255)

                                                                                                         cgAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCg                                                                        <  1:274024/83‑1 (MQ=255)

                                                                                                         cgAGTCGATGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATc                >  2:375057/1‑139 (MQ=255)

                                                                                                                 tGACCCGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGt        >  1:1020988/1‑139 (MQ=255)

                                                                                                                    cccGGGATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAAt     <  1:783552/139‑1 (MQ=255)

                                                                                                                       gggATATTTCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATgcg  >  2:677173/1‑139 (MQ=255)

TGACAGTGCTGTGAATCAACTGAATGAACCCTGGCCGGATTTAATTCTCCTCGACTGGATGTTACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTCCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCG  >  NC_000913/417246‑417503

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A