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
A2 F1 I2 R1	764	42.0	2018750	95.5%	1927906	109.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,018,530	(C)_6→7	coding (145/1128 nt)	fliK →	flagellar hook‑length control protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,018,524	1	.	C	100.0%	94.5 / NA	27	A47P (GCC→CCC)	fliK	flagellar hook‑length control protein
Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (14/13); total (14/13)

CTTGATTACCGCCGACGTTGACACCACCACATTGCCTGGCGGCAAAGCCAGCGATGCTGCACAAGATTTTCTCGCGTTGTTGAGCGAAGCATTAGCAGGCGAGACAACTACCGACAAAGCGG‑CCCCCCAGTTGCTGGTGGCAACAGATAAGCCCACGACAAAAGGCGAGCCGCTGATCAGCGATATTGTTTCCGACGCGCAACAAGCTAATTTACTGATCCCTGTGGATGAAACACCGCCTGTCAT  >  NC_000913/2018403‑2018648

cTTGATTACCGCCGACGTTGACACCACCACATTGCCTGGCGGCAAAGCCAGCGATGCTGCACAAGATTTTCTCGCGTTGTTGAGCGAAGCATTAGCAGGCGAGACAACTACCGACAAAGCGGCCCCCCCAGTTGCtggt                                                                                                              <  1:496089/139‑1 (MQ=255)

    aTTACCGCCGACGTTGACACCACCACATTGCCTGGCGGCAAAGCCAGCGATGCTGCACAAGATTTTCTCGCGTTGTTGAGCGAAGCATTAGCAGGCGAGACAACTACCGACAAAGCGG‑cccccccag                                                                                                                     <  2:116698/127‑4 (MQ=255)

    aTTACCGCCGACGTTGACACCACCACATTGCCTGGCGGCAAAGCCAGCGATGCTGCACAAGATTTTCTCGCGTTGTTGAGCGAAGCATTAGCAGGCGAGACAACTACCGACAAAGCGG‑cccccccag                                                                                                                     >  1:116698/1‑124 (MQ=255)

                      accaccacATTGCCTGGCGGCAAAGCCAGCGATGCTGCACAAGATTTTCTCGCGTTGTTGAGCGAAGCATTAGCAGGCGAGACAACTACCGACAAAGCGGCCCCCCCAGTTGCTGGTGGCAACAGAt                                                                                                    <  2:615471/127‑1 (MQ=255)

                      accaccacATTGCCTGGCGGCAAAGCCAGCGATGCTGCACAAGATTTTCTCGCGTTGTTGAGCGAAGCATTAGCAGGCGAGACAACTACCGACAAAGCGGCCCCCCCAGTTGCTGGTGGCAACAGAt                                                                                                    >  1:615471/1‑127 (MQ=255)

                          ccacATTGCCTGGCGGCAAAGCCAGCGATGCTGCACAAGATTTTCTCGCGTTGTTGAGCGAAGCATTAGCAGGCGAGACAACTACCGACAAAGCGGCCCCCCCAGTTGCTGGTGGCaa                                                                                                         >  2:986977/1‑118 (MQ=255)

                          ccacATTGCCTGGCGGCAAAGCCAGCGATGCTGCACAAGATTTTCTCGCGTTGTTGAGCGAAGCATTAGCAGGCGAGACAACTACCGACAAAGCGGCCCCCCCAGTTGCTGGTGGCaa                                                                                                         <  1:986977/118‑1 (MQ=255)

                             caTTGCCTGGCGGCAAAGCCAGCGATGCTGCACAAGATTTTCTCGCGTTGTTGAGCGAAGCATTAGCAGGCGAGACAACTACCGACAAAGCGG‑c                                                                                                                             <  1:3309/94‑1 (MQ=255)

                             caTTGCCTGGCGGCAAAGCCAGCGATGCTGCACAAGATTTTCTCGCGTTGTTGAGCGAAGCATTAGCAGGCGAGACAACTACCGACAAAGCGG‑c                                                                                                                             >  2:3309/1‑94 (MQ=255)

                                  ccTGGCGGCAAAGCCAGCGATGCTGCACAAGATTTTCTCGCGTTGTTGAGCGAAGCATTAGCAGGCGAGACAACTACCGACAAAGCGGCCCCCCCAGTTGCTGGTGGCa                                                                                                          <  2:529471/109‑1 (MQ=255)

                                  ccTGGCGGCAAAGCCAGCGATGCTGCACAAGATTTTCTCGCGTTGTTGAGCGAAGCATTAGCAGGCGAGACAACTACCGACAAAGCGGCCCCCCCAGTTGCTGGTGGCa                                                                                                          >  1:529471/1‑109 (MQ=255)

                                     ggcggcAAAGCCAGCGATGCTGCACAAGATTTTCTCGCGTTGTTGAGCGAAGCATTAGCAGGCGAGACAACTACCGACAAAGCGGCCCCCCCAGTTGCTGGTGGCAACAGATAAGCCCACGACAAAAGGCGAGCCGCTg                                                                         >  2:522833/1‑139 (MQ=255)

                                            aaGCCAGCGATGCTGCACAAGATTTTCTCGCGTTGTTGAGCGAAGCATTAGCAGGCGAGACAACTACCGACAAAGCGGCCCCCCCAGTTGCTGGTGGCAACAGATAAGCCCACGACAAAAGGCGAGCCGCTGATCAGCg                                                                  >  2:409079/1‑139 (MQ=255)

                                                           cacaAGATTTTCTCGCGTTGTTGAGCGAAGCATTAGCAGGCGAGACAACTACCGACAAAGCGGCCCCCCCAGTTGCTGGTGGCAACAGATAAGCCCACGACAAAAGGCGAGCCGCTGATCAGCGATATTGTTTCCGAcg                                                   <  1:409079/139‑1 (MQ=255)

                                                                                     gAAGCATTAGCAGGCGAGACAACTACCGACAAAGCGGCCCCCCCAGTTGCTGGTGGCAACAGATAAGCCCACGACAAAAGGCGAGCCGCTGATCAGCGATATTGTTTCCGACGCGCAACAAGCTAATTTACTGATCCCt                         <  2:458329/139‑1 (MQ=255)

                                                                                         cATTAGCAGGCGAGACAACTACCGACAAAGCGGCCCCCCCAGTTGCTGGTGGCAACAGATAAGCCCACGACAAAAGGCGAGCCGCTGATCAGCGATATTGTTTCCGACGCGCAACAAGCTAATTTACTGATCCCTGTgg                     >  2:189311/1‑139 (MQ=255)

                                                                                          aTTAGCAGGCGAGACAACTACCGACAAAGCGGCCCCCCCAGTTGCTGGTGGCAACAGATAAGCCCACGACAAAAGGCGAGCCGCTGATCAGCGATATTGTTTCCGACGCGCAACAAGCTAATTTACTGATCCCTGTGGa                    <  1:189311/139‑1 (MQ=255)

                                                                                            tAGCAGGCGAGACAACTACCGACAAAGCGGCCCCCCCAGTTGCTGGTGGCAACAGATAAGCCCACGACAAAAGGCGAGCCGCTGATCAGCGATATTGTTTCCGACGCGCAACAAGCTAATTTACTGATCCCTGTGGATg                  >  1:979439/1‑139 (MQ=255)

                                                                                               cAGGCGAGACAACTACCGACAAAGCGGCCCCCCCAGTTGCTGGTGGCAACAGATAAGCCCACGACAAAAGGCGAGCCGCTGATCAGCGATATTGTTTCCGACGCGCAACAAGCTAATTTACTGATCCCTGTGGATGaaa               <  2:979439/139‑1 (MQ=255)

                                                                                                 ggCGAGACAACTACCGACAAAGCGGCCCCCCCAGTTGCTGGTGGCAACAGATAAGCCCACGACAAAAGGCGAGCCGCTGATCAGCGATATTGTTTCCGACGCGcaaca                                            >  1:730769/1‑108 (MQ=255)

                                                                                                 ggCGAGACAACTACCGACAAAGCGGCCCCCCCAGTTGCTGGTGGCAACAGATAAGCCCACGACAAAAGGCGAGCCGCTGATCAGCGATATTGTTTCCGACGCGcaaca                                            <  2:730769/108‑1 (MQ=255)

                                                                                                   cGAGACAACTACCGACAAAGCGGCCCCCCCAGTTGCTGGTGGCAACAGATAAGCCCACGACAAAAGGCGAGCCGCTGATCAGCGATATTGTTTCCGACGCGCAACAAg                                          <  1:733115/108‑1 (MQ=255)

                                                                                                   cGAGACAACTACCGACAAAGCGGCCCCCCCAGTTGCTGGTGGCAACAGATAAGCCCACGACAAAAGGCGAGCCGCTGATCAGCGATATTGTTTCCGACGCGCAACAAg                                          >  2:733115/1‑108 (MQ=255)

                                                                                                   cGAGACAACTACCGACAAAGCGGCCCCCCCAGTTGCTGGTGGCAACAGATAAGCCCACGACAAAAGGCGAGCCGCTGATCAGCGATATTGTTTCCGACGCGCAACAAGCTAATTTACTGATCCCTGTGGATGAAACAcc           >  2:232530/1‑139 (MQ=255)

                                                                                                            tACCGACAAAGCGGCCCCCCCAGTTGCTGGTGGCaa                                                                                                         <  1:962369/36‑1 (MQ=255)

                                                                                                            tACCGACAAAGCGGCCCCCCCAGTTGCTGGTGGCaa                                                                                                         >  2:962369/1‑36 (MQ=37)

                                                                                                            tACCGACAAAGCGGCCCCCCCAGTTGCTGGTGGCAACAGATAAGCCCACGACAAAAGGCGAGCCGCTGATCAGCGATATTGTTTCCGACGCGCAACAAGCTAATTTACTGATCCCTGTGGATGAAACACCGCCTGtcat  >  2:831953/1‑139 (MQ=255)

                                                                                                                 aCAAAGCGGCCCCCCCAGTTGCTGGTGGCAACAGATAAGCCCACGACAAAAGGCGAGCCGCTGATCAGCGATATTGTTTCCGACGCGCAACAAGCTAATTTACTGATCCCTGTGGATGAAACACCGCCt       >  2:282480/1‑129 (MQ=255)

                                                                                                                 aCAAAGCGGCCCCCCCAGTTGCTGGTGGCAACAGATAAGCCCACGACAAAAGGCGAGCCGCTGATCAGCGATATTGTTTCCGACGCGCAACAAGCTAATTTACTGATCCCTGTGGATGAAACACCGCCt       <  1:282480/129‑1 (MQ=255)

                                                                                                                     aGCGGCCCCCCCAGTTGCTGGTGGCAACAGATAAGCCCACGACAAAAGGCGAGCCGCTGATCAGCGATATTGTTTCCGACGCGCAACAAGCTAAt                                     >  2:213613/1‑95 (MQ=255)

                                                                                                                     aGCGGCCCCCCCAGTTGCTGGTGGCAACAGATAAGCCCACGACAAAAGGCGAGCCGCTGATCAGCGATATTGTTTCCGACGCGCAACAAGCTAAt                                     <  1:213613/95‑1 (MQ=255)

CTTGATTACCGCCGACGTTGACACCACCACATTGCCTGGCGGCAAAGCCAGCGATGCTGCACAAGATTTTCTCGCGTTGTTGAGCGAAGCATTAGCAGGCGAGACAACTACCGACAAAGCGG‑CCCCCCAGTTGCTGGTGGCAACAGATAAGCCCACGACAAAAGGCGAGCCGCTGATCAGCGATATTGTTTCCGACGCGCAACAAGCTAATTTACTGATCCCTGTGGATGAAACACCGCCTGTCAT  >  NC_000913/2018403‑2018648

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