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 I1 R1	748	32.0	1685426	92.6%	1560704	103.9

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%	85.0 / NA	25	A47P (GCC→CCC)	fliK	flagellar hook‑length control protein
Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (9/16); total (9/16)

GCGCCCTTGATTACCGCCGACGTTGACACCACCACATTGCCTGGCGGCAAAGCCAGCGATGCTGCACAAGATTTTCTCGCGTTGTTGAGCGAAGCATTAGCAGGCGAGACAACTACCGACAAAGCGG‑CCCCCCAGTTGCTGGTGGCAACAGATAAGCCCACGACAAAAGGCGAGCCGCTGATCAGCGATATTGTTTCCGACGCGCAACAAGCTAATTTACTGATCCCTGTGGATGAAACACCGCCTGTCATCAACG  >  NC_000913/2018398‑2018653

gcgcCCTTGATTACCGCCGACGTTGACACCACCACATTGCCTGGCGGCAAAGCCAGCGATGCTGCACAAGATTTTCTCGCGTTGTTGAGCGAAGCATTAGCAGGCGAGACAACTACCGACAAAGCGGCCCCCCCAGTTg                                                                                                                        <  2:58239/139‑1 (MQ=255)

     cTTGATTACCGCCGACGTTGACACCACCACATTGCCTGGCGGCAAAGCCAGCGATGCTGCACAAGATTTTCTCGCGTTGTTGAGCGAAGCATTAGCAGGCGAGACAACTACCGACAAAGCGGCCCCCCCAGTTGCtggt                                                                                                                   <  1:83294/139‑1 (MQ=255)

         aTTACCGCCGACGTTGACACCACCACATTGCCTGGCGGCAAAGCCAGCGATGCTGCACAAGATTTTCTCGCGTTGTTGAGCGAAGCATTAGCAGGCGAGACAACTACCGACAAAGCGGCCCCCCCAGTTGCTGGTGGCa                                                                                                               <  2:204487/139‑1 (MQ=255)

              cgccgACGTTGACACCACCACATTGCCTGGCGGCAAAGCCAGCGATGCTGCACAAGATTTTCTCGCGTGGTTGAGCGAAGCATTAGCAGGCGAGACAACTACCGACAAAGCGGCCCCCCCAGTTGCTGGTGGCGACAGa                                                                                                          >  1:520442/1‑139 (MQ=255)

                    cGTTGAGACCACCACATTGCCTGGCGGCAAAGCCAGCGATGCTGCACAAGATTTTCTCGCGTTGTTGAGCGAAGCATTAGCAGGCGAGACAACTACCGACAAAGCGGCCCCCCCAGTTGCTGGTGGCAACAGATAAGcc                                                                                                    >  2:818944/1‑139 (MQ=255)

                                       ccTGGCGGCAAAGCCAGCGATGCTGCACAAGATTTTCTCGCGTTGTTGAGCGAAGCATTAGCAGGCGAGACAACTACCGACAAAGCGGCCCCCCCAGTTGCtgg                                                                                                                    <  2:52888/104‑1 (MQ=255)

                                       ccTGGCGGCAAAGCCAGCGATGCTGCACAAGATTTTCTCGCGTTGTTGAGCGAAGCATTAGCAGGCGAGACAACTACCGACAAAGCGGCCCCCCCAGTTGCtgg                                                                                                                    >  1:52888/1‑104 (MQ=255)

                                       ccTGGCGGCAAAGCCAGCGATGCTGCACAAGATTTTCTCGCGTTGTTGAGCGAAGCATTAGCAGGCGAGACAACTACCGACAAAGCGGCCCCCCCAGTTGCTGGTGGCAACAGATAAGCCCACGACAAAAGGCGAGCCg                                                                                 >  1:89705/1‑139 (MQ=255)

                                            cggcAAAGCCAGCGATGCTGCACAAGATTTTCTCGCGTTGTTGAGCGAAGCATTAGCAGGCGAGACAACTACCGACAAAGCGGCCCCCCCAGTTGCTGGTGGCAACAGATAAGCCCACGACAAAAGGCGAGCCGCTGAt                                                                            <  1:2914/139‑1 (MQ=255)

                                                    ccAGCGATGCTGCACAAGATTTTCTCGCGTTGTTGAGCGAAGCATTAGCAGGCGAGACAACTACCGACAAAGCGGCCCCCCCAGTTGCTGGTGGCAACAGATAAGCCCACGACAAAAGGCGAGCCGCTGATCAGCGata                                                                    <  1:818944/139‑1 (MQ=255)

                                                           tgctgcACAAGATTTTCTCGCGTTGTTGAGCGAAGCATTAGCAGGCGAGACAACTACCGACAAAGCGGCCCCCCCAGTTGCTGGTGGCAACAGATAAGCCCACGACAAAAGGCGAGCCGCTGATCAGCGATATTGTTTc                                                             <  2:89705/139‑1 (MQ=255)

                                                                cacaAGATTTTCTCGCGTTGTTGAGCGAAGCATTAGCAGGCGAGACAACTACCGACAAAGCGGCCCCCCCAGTTGCTGGTGGCAACAGATAAGCCCACGACAAAAGGCGAGCCGCTGATCAGCGATATTGTTTCCGAcg                                                        <  1:88454/139‑1 (MQ=255)

                                                                     gATTTTCTCGCGTTGTTGAGCGAAGCATTAGCAGGCGAGACAACTACCGACAAAGCGGCCCCCCCAGTTGCtgg                                                                                                                    >  1:782389/1‑74 (MQ=255)

                                                                     gATTTTCTCGCGTTGTTGAGCGAAGCATTAGCAGGCGAGACAACTACCGACAAAGCGGCCCCCCCAGTTGCtgg                                                                                                                    <  2:782389/74‑1 (MQ=255)

                                                                         ttCTGGCGTTGTTGAGCGAAGCATTAGCAGGCGAGACAACTACCGACAAAGCGGCCCCCCCAGTTGCTGGTGGCAACAGATAAGCCCACGACAAAAGGCGAGCCGCTGATCAGCGATATTGTTTCCGACGCGCAACAAg                                               <  2:266940/139‑1 (MQ=255)

                                                                          tctcGCGTTGTTGAGCGAAGCATTAGCAGGCGAGACAACTACCGACAAAGCGGCCCCCCCAGTTGCtggt                                                                                                                   >  2:419284/1‑70 (MQ=255)

                                                                          tctcGCGTTGTTGAGCGAAGCATTAGCAGGCGAGACAACTACCGACAAAGCGGCCCCCCCAGTTGCtggt                                                                                                                   <  1:419284/70‑1 (MQ=255)

                                                                                      gAGCGAAGCATTAGCAGGCGAGACAACTACCGACAAAGCGGCCCCCCCAGTTGATGGTGGCAACAGATAAGCCCACGACAAAAGGCGAGCCGCTGATCAGCGATATTGTTTCCGACGCGCAACAAGCTAATTTACTGag                                  <  2:522591/139‑2 (MQ=255)

                                                                                              cATTAGCAGGCGAGACAACTACCGACAAAGCGGCCCCCCCAGTTGCTGGTGGCAACAGATAAGccc                                                                                                   <  2:281905/66‑1 (MQ=255)

                                                                                              cATTAGCAGGCGAGACAACTACCGACAAAGCGGCCCCCCCAGTTGCTGGTGGCAACAGATAAGccc                                                                                                   >  1:281905/1‑66 (MQ=255)

                                                                                                 tAGCAGGCGAGACAACTACCGACAAAGCGGCCCCCCCAGTTGCTGGTGGCAACAGATAAGCCCACGACAAAAGGCGAGCCGCTGATCAGCGATATTGTTTCCGACGCGCAACAAGCTAATTTACTGATCCCTGTGGATg                       >  1:169147/1‑139 (MQ=255)

                                                                                                      ggCGAGACAACTACCGACAAAGCGGCCCCCCCAGTTGCTGGTGGCAACAGATAAGCCCACGACAAAAGGCGAGCCg                                                                                 <  2:314821/76‑1 (MQ=255)

                                                                                                      ggCGAGACAACTACCGACAAAGCGGCCCCCCCAGTTGCTGGTGGCAACAGATAAGCCCACGACAAAAGGCGAGCCg                                                                                 >  1:314821/1‑76 (MQ=255)

                                                                                                       gCGAGACAACTACCGACAAAGCGGCCCCCCCAGTTGCTGGTGGCAACAGATAAGCCAACGCCAAAAGGCGAGCCGCTGATCAGCGATATTGTTTCCGACGCGCAACAAGCTAATTTACTCATCCCTGTGGATGAAacac                 <  2:642906/139‑1 (MQ=255)

                                                                                                                      aCAAAGCGGCCCCCCCAGTTGCTGGTGGCAACAGATAAGCCCACGACAAAAGGCGAGCCGCTGATCAGCGATATTGTTTCCGACGCGCAACAAGCTAATTTACTGATCCCTGTGGATGAAACACCGCCTGTCATCAacg  <  2:305797/139‑1 (MQ=255)

GCGCCCTTGATTACCGCCGACGTTGACACCACCACATTGCCTGGCGGCAAAGCCAGCGATGCTGCACAAGATTTTCTCGCGTTGTTGAGCGAAGCATTAGCAGGCGAGACAACTACCGACAAAGCGG‑CCCCCCAGTTGCTGGTGGCAACAGATAAGCCCACGACAAAAGGCGAGCCGCTGATCAGCGATATTGTTTCCGACGCGCAACAAGCTAATTTACTGATCCCTGTGGATGAAACACCGCCTGTCATCAACG  >  NC_000913/2018398‑2018653

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 31 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A