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
A10 F1 I2 R1	757	38.1	1607544	96.5%	1551279	117.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,012,553	Δ1 bp	intergenic (+160/+61)	yqeA → / ← yqeB	putative amino acid kinase/XdhC‑CoxI family protein with NAD(P)‑binding Rossman fold

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,012,552	0	G	.	100.0%	129.4 / NA	32	intergenic (+159/+62)	yqeA/yqeB	putative amino acid kinase/XdhC‑CoxI family protein with NAD(P)‑binding Rossman fold
Reads supporting (aligned to +/- strand): ref base G (0/0); new base . (15/17); total (15/17)

CCATCCGGCCAAAGATTGTCAAGTAAGTGCGCTTTGTTGATGCCGGATGCGGCGCGAGCGCCTTATCCGTCCTACAAAACATCGCAAATTCAATAGATTGCAATGCACTTGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTTGGCGTTTGTCATCAGTCTCAGGCCGGGTGGGTAATACCATCCGGCCATTTTCATTTAAGCCACTTCCAGCACTTCTTTTGTCGCTTTCACGCCCTGATGCATCAACATCATTAACGCCTCAAGTACG  >  NC_000913/3012416‑3012686

ccATCCGGCCAAAGATTGTCAAGTAAGTGCGCTTTGTTGATGCCGGATGCGGCGCGAGCGCCTTATCCGTCCTACAAAACATCGCAAATTCAATAGATTGCAATGCACTTGTAGGCCTGATAAGCGTAGCGCATCAgca                                                                                                                                      >  2:1670/1‑137 (MQ=255)

ccATCCGGCCAAAGATTGTCAAGTAAGTGCGCTTTGTTGATGCCGGATGCGGCGCGAGCGCCTTATCCGTCCTACAAAACATCGCAAATTCAATAGATTGCAATGCACTTGTAGGCCTGATAAGCGTAGCGCATCAgca                                                                                                                                      >  1:687891/1‑137 (MQ=255)

 cATCCGGCCAAAGATTGTCAAGTAAGTGCGCTTTGTTGATGCCGGATGCGGCGCGAGCGCCTTATCCGTCCTACAAAACATCGCAAATTCAATAGATTGCAATGCACTTGTAGGCCTGATAAGCGTAGCGCATCAgcaa                                                                                                                                     <  2:687891/139‑4 (MQ=255)

   tCCGGCCAAAGATTGTCAAGTAAGTGCGCTTTGTTGATGCCGGATGCGGCGCGAGCGCCTTATCCGTCCTACAAAACATCGCAAATTCAATAGATTGCAATGCACTTGTAGGCCTGATAAGCGTAGCGCATCA‑GCAAtt                                                                                                                                  >  2:207488/1‑139 (MQ=255)

    ccGGCCAAAGATTGTCAAGTAAGTGCGCTTTGTTGATGCCGGATGCGGCGCGAGCGCCTTATCCGTCCTACAAAACATCGCAAATTCAATAGATTGCAATGCACTTGTAGGCCTGATAAGCGTAGCGCATCA‑GCAAttt                                                                                                                                 >  2:671781/1‑139 (MQ=255)

                 gTCAAGTAAGTGCGCTTTGTTGATGCCGGATGCGGCGCGAGCGCCTTATCCGTCCTACAAAACATCGCAAATTCAATAGATTGCAATGCACTTGTAGGCCTGATAAGCGTAGCGCATCA‑GCAATTTGGCGTTTGtcatc                                                                                                                    >  1:152969/1‑139 (MQ=255)

                          gtGCGCTTTGTTGATGCCGGATGCGGCGCGAGCGCCTTATCCGTCCTACAAAACATCGCAAATTCAATAGATTGCAATGCACTTGTAGGCCTGATAAGCGTAGCGCATCA‑GCAATTTGGCGTTTGTCATCAGTCTCAgg                                                                                                           >  2:453009/1‑139 (MQ=255)

                              gcTTTGTTGATGCCGGATGCGGCGCGAGCGCCTTATCCGTCCTACAAAACATCGCAAATTCAATAGATTGCAATGCACTTGTAGGCCTGATAAGCGTAGCGCATCA‑GCAATTTGGCGTTTGTCATCAGTCTCAGGCCgg                                                                                                       <  1:670563/139‑1 (MQ=255)

                                                  ggcgCGAGCGCCTTATCCGTCCTACAAAACATCGCAAATTCAATAGATTGCAATGCACTTGTAGGCCTGATAAGCGTAGCGCATCA‑GCAATTTGGCGTTTGTCATCAGTCTCAGGCCgg                                                                                                       <  1:614033/119‑1 (MQ=255)

                                                  ggcgCGAGCGCCTTATCCGTCCTACAAAACATCGCAAATTCAATAGATTGCAATGCACTTGTAGGCCTGATAAGCGTAGCGCATCA‑GCAATTTGGCGTTTGTCATCAGTCTCAGGCCgg                                                                                                       >  2:614033/1‑119 (MQ=255)

                                                                     tCCTACAAAACATCGCAAATTCAATAGATTGCAATGCACTTGTAGGCCTGATAAGCGTAGCGCATCA‑GCAATTTGGCGTTTGtcat                                                                                                                     <  1:585774/86‑1 (MQ=255)

                                                                     tCCTACAAAACATCGCAAATTCAATAGATTGCAATGCACTTGTAGGCCTGATAAGCGTAGCGCATCA‑GCAATTTGGCGTTTGtcat                                                                                                                     >  2:585774/1‑86 (MQ=255)

                                                                          cAAAACATCGCAAATTCAATAGATTGCAATGCACTTGTAGGCCTGATAAGCGTAGCGCATCA‑GCAATTTGGCGTTTGTCATCAGTCTCAGGCCGGGTGGGTAATACCATCCGGCCATTTTCATTTAAGCCACTTCCAGc                                                           >  2:646045/1‑139 (MQ=255)

                                                                                  cGCAAATTCAATAGATTGCAATGCACTTGTAGGCCTGATAAGCGTAGCGCATCA‑GCAATTTGGCGTTTGTCATCAGTCTCAGGCCGGGTGGGTAATACCATCCGGCCATTTTCATTTAAGCCACTTCCAGCACTTCttt                                                   >  1:107598/1‑139 (MQ=255)

                                                                                           aaTAGATTGCAATGCACTTGTAGGCCTGATAAGCGTAGCGCATCA‑GCAATTTGGCGTTTGTCATCAGTCTCAGGCCGGGTGGGTAATACCATCCGGCCATTTTCATTTAAGCCACTTCCAGCACTTCTTTTGTCGCttt                                          <  1:339380/139‑1 (MQ=255)

                                                                                            aTAGATTGCAATGCACTTGTAGGCCTGATAAGCGTAGCGCATCA‑GCAATTTGGCGTTTGTCATCAGTCTCAGGCCGGGTGGGTAATACCATCCGGCCATTTTCATTTAAGCCACTTCCAGCACTTCTTTTGTCGCTTTc                                         <  2:168490/139‑1 (MQ=255)

                                                                                                 ttGCAATGCACTTGTAGGCCTGATAAGCGTAGCGCATCA‑GCAATTTGGCGTTTGTCATCAGTCTCAGGCCGGGTGGGTAATACCATCCGGCCATTTTCATTTAAGCCACTTCCAGCACTTCTTTTGTCGCTTTCACGcc                                    <  2:152969/139‑1 (MQ=255)

                                                                                                    cAATGCACTTGTAGGCCTGATAAGGGTAGCGATTCA‑GAAAATTGGCGTTTGTCATCAGTCTCAGGCCGGGTGGGTAATACCATCCGGCCATTTTCATTTAAGCCACTTCCAGCACTTCTTTTGACGCTTTCACGCCCTg                                 <  1:1670/139‑1 (MQ=255)

                                                                                                         cACTTGTAGGCCTGATAAGCGTAGCGCATCA‑GCAATTTGGCGTTTGTCATCAGTCTCAGGCCGGGTGGGTAATACCATCCGGCCATTTTCATTTAAGCCACTTCCAGCACTTCTTTTGTCGCTTTCACGCCCTGATGCa                            <  1:207488/139‑1 (MQ=255)

                                                                                                           cTTGTAGGCCTGATAAGCGTAGCGCATCA‑GCAATTTGGCGTTTGTCATCAGTCTCAGGCCGGGTGGGTAATACCATCCGGCCATTTTCATTTAAGCCACTTCCAGCACTTCTTTTGTCGCTTTCACGCCCTGATGCATc                          <  1:646045/139‑1 (MQ=255)

                                                                                                           cTTGTAGGCCTGATAAGCGTAGCGCATCA‑GCAATTTGGCGTTTGTCATCAGTCTCAGGCCGGGTGGGTAATACCATCCGGCCATTTTCATTTAAGCCACTTCCAGCACTTCTTTTGTCGCTTTCACGCCCTGATGCATc                          <  1:675184/139‑1 (MQ=255)

                                                                                                                 ggCCTGATAAGCGTAGCGCATCA‑GCAATTTGGCGTTTGTCATCAGTCTCAGGCCGGGTGGGTAATACCATCCGGCCATTTTCATTTAAGCCACTTCCAGCACTTCTTTTGTCGCTTTCACGCCCTGATGCATCAAcatc                    >  1:396723/1‑139 (MQ=255)

                                                                                                                    cTGATAAGCGTAGCGCATCA‑GCAATTTGGCGTTTGTCATCAGTCTCAGGCCGGGTGGGTAATACCATCCgg                                                                                     >  2:702185/1‑71 (MQ=255)

                                                                                                                    cTGATAAGCGTAGCGCATCA‑GCAATTTGGCGTTTGTCATCAGTCTCAGGCCGGGTGGGTAATACCATCCgg                                                                                     <  1:702185/71‑1 (MQ=255)

                                                                                                                    cTGATAAGCGTAGCGCATCA‑GCAATTTGGCGTTTGTCATCAGTCTCAGGCCGGGTGGGTAATACCATCCGGCCATTTTCATTTAAGCCACTTCCAGCACTTCTTTTGTCGCTTTCACGCCCTGATGCATCAACATCAtt                 >  2:275580/1‑139 (MQ=255)

                                                                                                                    cTGATAAGCGTAGCGCATCA‑GCAATTTGGCGTTTGTCATCAGTCTCAGGCCGGGTGGGTAATACCATCCGGCCATTTTCATTTAAGCCACTTCCAGCACTTCTTTTGTCGCTTTCACGCCCTGATGCATCAACATCAtt                 <  1:453009/139‑1 (MQ=255)

                                                                                                                      gATAAGCGTAGCGCATCA‑GCAATTTGGCGTTTGTCATCAGtct                                                                                                               <  1:69899/43‑1 (MQ=17)

                                                                                                                      gATAAGCGTAGCGCATCA‑GCAATTTGGCGTTTGTCATCAGtct                                                                                                               >  2:69899/1‑43 (MQ=17)

                                                                                                                      gATAAGCGTAGCGCATCA‑GCAATTTGGCGTTTGTCATCAGTCTCAGGCCGGGTGGGTAATACCATCCGGCCATTTTCATTTAAg                                                                      >  2:433249/1‑84 (MQ=255)

                                                                                                                      gATAAGCGTAGCGCATCA‑GCAATTTGGCGTTTGTCATCAGTCTCAGGCCGGGTGGGTAATACCATCCGGCCATTTTCATTTAAg                                                                      <  1:433249/84‑1 (MQ=255)

                                                                                                                        tAAGCGTAGCGCATCA‑GCAATTTGGCGTTTGTCATCAGTCTCAGGCCgggtgg                                                                                                   <  1:725955/53‑1 (MQ=255)

                                                                                                                        tAAGCGTAGCGCATCA‑GCAATTTGGCGTTTGTCATCAGTCTCAGGCCgggtgg                                                                                                   >  2:725955/1‑53 (MQ=255)

                                                                                                                            cGTAGCGCATCA‑GCAATTTGGCGTTTGTCATCAGTCTCAGGCCGGGTGGGTAATACCATCCGGCCATTTTCATTTAAGCCACTTCCAGCACTTCTTTTGTCGCTTTCACGCCCTGATGCATCAACATCATTAACGCCTc         >  2:149594/1‑139 (MQ=255)

                                                                                                                                   cATCA‑GCAATTTGGCGTTTGTCATCAGTCTCAGGCCGGGTGGGTAATACCATCCGGCCATTTTCATTTAAGCCACTTCCAGCACTTCTTTTGTCGCTTTCACGCCCTGATGCATCAACATCATTAACGCCTCAAGTAcg  <  1:671781/139‑1 (MQ=255)

                                                                                                                                   cATCA‑GCAATTTGGCGTTTGTCATCAGTCTCAGGCCGGGTGGGTAATACCATCCGGCCATTTTCATTTAAGCCACTTCCAGCACTTCTTTTGTCGCTTTCACGCCCTGATGCATCAACATCATTAACGCCTCAAGTAcg  <  1:410511/139‑1 (MQ=255)

CCATCCGGCCAAAGATTGTCAAGTAAGTGCGCTTTGTTGATGCCGGATGCGGCGCGAGCGCCTTATCCGTCCTACAAAACATCGCAAATTCAATAGATTGCAATGCACTTGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTTGGCGTTTGTCATCAGTCTCAGGCCGGGTGGGTAATACCATCCGGCCATTTTCATTTAAGCCACTTCCAGCACTTCTTTTGTCGCTTTCACGCCCTGATGCATCAACATCATTAACGCCTCAAGTACG  >  NC_000913/3012416‑3012686

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 31 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A