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
A16 F60 I1 R1	18	40.4	1393842	98.9%	1378509	138.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,530,076	(A)_7→6	coding (155/483 nt)	ydcD →	uncharacterized protein YdcD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,530,070	0	A	.	97.7%	173.8 / ‑2.3	44	coding (149/483 nt)	ydcD	uncharacterized protein YdcD
Reads supporting (aligned to +/- strand): ref base A (0/1); new base . (19/24); total (19/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TATTAGAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATAAAACACCAAAGAGCGTTGAGATATATCTTTCTGAAAAAAATATTATTTATAAAATAATTAATGACCAAAAAATTAGTAGAGGGAATGGTCATTTTATAAGTATAATGGTTAATAATTACAGGACGCACTGTGGAGTGGTTGATATAAATCTTAATTTTTTCAATGAT  >  NC_000913/1529933‑1530203

tattaGAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATAAAACACCAAAGAGCGTTGAGATATATCTTTCTGaaa                                                                                                                                     <  2:296302/140‑1 (MQ=255)

            aCTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATAAAACACCAAAGAGCGTTGAGATATATCTTTCTG‑AAAAAATAttattta                                                                                                                        >  1:66694/1‑140 (MQ=255)

             cTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATAAAACACCAAAGAGCGTTGAGATATATCTTTCTG‑AAAAAATAttatttat                                                                                                                       <  1:618328/140‑1 (MQ=255)

                                 ccTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATAAAACACCAAAGAGCGTTGAGATATATCTTTCTG‑AAAAAATATTATTTATAAAATAATTAATGACCaaaa                                                                                                   <  1:623167/140‑1 (MQ=255)

                                   tttGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATAAAACACCAAAGAGCGTTGAGATATATCTTTCTG‑AAAAAATATTATTTATAAAATAATTAATGACCaaaaaa                                                                                                 >  2:353171/1‑140 (MQ=255)

                                    ttGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATAAAACACCAAAGAGCGTTGAGATATATCTTTCTG‑AAAAAATATTATTTATAAAATAATTAATGACCAAAAAAt                                                                                                <  2:61918/140‑1 (MQ=255)

                                     tGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATAAAACACCAAAGAGCGTTGAGATATATCTTTCTG‑AAAAAATATTATTTATAAAATAATTAATGACCAAAAAAtt                                                                                               <  2:477161/140‑1 (MQ=255)

                                                 gttTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATAAAACACCAAAGAGCGTTGAGATATATCTTTCTG‑AAAAAATATTATTTATAAAATAATTAATGACCAAAAAATTAGTAGAGGGAAt                                                                                   >  1:6678/1‑140 (MQ=255)

                                                    tACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATAAAACACCAAAGAGCGTTGAGATATATCTTTCT‑AAAAAAATATTATTTATAAAATAATTAATGACCAAAAAATTAGTAGAGGGAATGGt                                                                                <  2:275752/140‑1 (MQ=255)

                                                         tGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATAAAACACCAAAGAGCGTTGAGATATATCTTTCTG‑AAAAAATATTATTTATAAAATAATTAATGACCAAAAAATTAGTAGAGGGAATGGTCAttt                                                                           >  2:195827/1‑140 (MQ=255)

                                                         tGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATAAAACACCAAAGAGCGTTGAGATATATCTTTCTG‑AAAAAATATTATTTATAAAATAATTAATGACCAAAAAATTAGTAGAGGGAATGGTCAttt                                                                           >  1:459865/1‑140 (MQ=255)

                                                            gTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATAAAACACCAAAGAGCGTTGAGATATATCTTTCTG‑AAAAAATATTATTTATAAAATAATTAATGACCAAAAAATTAGTAGAGGGAATGGTCATTTtat                                                                        <  2:516810/140‑1 (MQ=255)

                                                            gTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATAAAACACCAAAGAGCGTTGAGATATATCTTTCTG‑AAAAAATATTATTTATAAAATAATTAATGACCAAAAAATTAGTAGAGGGAATGGTCATTTtat                                                                        <  1:353171/140‑1 (MQ=255)

                                                            gTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATAAAACACCAAAGAGCGTTGAGATATATCTTTCTG‑AAAAAATATTATTTATAAAATAATTAATGACCAAAAAATTAGTAGAGGGAATGGTCATTTtat                                                                        <  1:629685/140‑1 (MQ=255)

                                                              ttGATAACAATTCAAATTCTGACATCGTATTTTATGGACATAAAACACCAAAGAGCGTTGAGATATATCTTTCTG‑AAAAAATATTATTTATAAAATAATTAATGACCAAAAAATTAGTAGAGGGAATGGTCATTTTATaa                                                                      <  1:116479/140‑1 (MQ=255)

                                                                gATAACAATTCAAATTCTGACATCGTATTTTATGGACATAAAACACCAAAGAGCGTTGAGATATATCTTTCTG‑AAAAAATATTATTTATAAAATAATTAATGACCAAAAAATTAGTAGAGGGAATGGTCATTTTATAAGt                                                                    >  2:468422/1‑140 (MQ=255)

                                                                gATAACAATTCAAATTCTGACATCGTATTTTATGGACATAAAACACCAAAGAGCGTTGAGATATATCTTTCTG‑AAAAAATATTATTTATAAAATAATTAATGACCAAAAAATTAGTAGAGGGAATGGTCATTTTATAAGt                                                                    >  2:354262/1‑140 (MQ=255)

                                                                 aTAACAATTCAAATTCTGACATCGTATTTTATGGACATAAAACACCAAAGAGCGTTGAGATATATCTTTCTG‑AAAAAATATTATTTATAAAATAATTAATGACCAAAAAATTAGTAGAGGGAATGGTCATTTTATAAGta                                                                   >  1:412124/1‑140 (MQ=255)

                                                                 aTAACAATTCAAATTCTGACATCGTATTTTATGGACATAAAACACCAAAGAGCGTTGAGATATATCTTTCTG‑AAAAAATATTATTTATAAAATAATTAATGACCAAAAAATTAGTAGAGGGAATGGTCATTTTATAAGta                                                                   >  1:90462/1‑140 (MQ=255)

                                                                   aaCAATTCAAATTCTGACATCGTATTTTATGGACATAAAACACCAAAGAGCGTTGAGATATATCTTTCTG‑AAAAAATATTATTTATAAAATAATTAATGACCAAAAAATTAGTAGAGGGAATGGTCATTTTATAAGtata                                                                 <  1:226340/140‑1 (MQ=255)

                                                                        ttCAAATTCTGACATCGTATTTTATGGACATAAAACACCAAAGAGCGTTGAGATATATCTTTCTG‑AAAAAATATTATTTATAAAATAATTAATGACCAAAAAATTAGTAGAGGGAATGGTCATTTTATAAGTATAATGGt                                                            >  1:236148/1‑140 (MQ=255)

                                                                           aaaTTCTGACATCGTATTTTATGGACATAAAACACCAAAGAGCGTTGAGATATATCTTTCTG‑AAAAAATATTATTTATAAAATAATTAATGACCAAAAAATTAGTAGAGGGAATGGTCATTTTATAAGTATAATGGTtaa                                                         <  2:236148/140‑1 (MQ=255)

                                                                             aTTCTGACATCGTATTTTATGGACATAAAACACCAAAGAGCGTTGAGATATATCTTTCTG‑AAAAAATATTATTTATAAAATAATTAATGACCAAAAAATTAGTAGAGGGAATGGTCATTTTATAAGTATAATGGTtaata                                                       >  1:519080/1‑140 (MQ=255)

                                                                                   aCATCGTATTTTATGGACATAAAACACCAAAGAGCGTTGAGATATATCTTTCTG‑AAAAAATATTATTTATAAAATAATTAATGACCAAAAAATTAGTAGAGGGAATGGTCATTTTATAAGTATAATGGTTAATAATTACa                                                 >  1:567667/1‑140 (MQ=255)

                                                                                     aTCGTATTTTATGGACATAAAACACCAAAGAGCGTTGAGATATATCTTTCTG‑AAAAAATATTATTTATAAAATAATTAATGACCAAAAAATTAGTAGAGGGAATGGTCATTTTATAAGTATAATGGTTAATAATTACAgg                                               <  2:90462/140‑1 (MQ=255)

                                                                                     aTCGTATTTTATGGACATAAAACACCAAAGAGCGTTGAGATATATCTTTCTG‑AAAAAATATTATTTATAAAATAATTAATGACCAAAAAATTAGTAGAGGGAATGGTCATTTTATAAGTATAATGGTTAATAATTACAgg                                               <  2:567667/140‑1 (MQ=255)

                                                                                       cGTATTTTATGGACATAAAACACCAAAGAGCGTTGAGATATATCTTTCTG‑AAAAAATATTATTTATAAAATAATTAATGACCAAAAAATTAGTAGAGGGAATGGTCATTTTATAAGTATAATGGTTAATAATTACAGGAc                                             <  2:6678/140‑1 (MQ=255)

                                                                                          aTTTTATGGACATAAAACACCAAAGAGGGTTGAGATATATCTTTCTG‑AAAAAATATTATTTATAAAATAATTAATGACCAAAAAATTAGTAGAGGGAATGGTCATTTTATAAGTATAATGGTTAATAATTACAGGACGCa                                          <  1:179676/140‑1 (MQ=255)

                                                                                          aTTTTATGGACATAAAACACCAAAGAGCGTTGAGATATATCTTTCTG‑AAAAAATATTATTTATAAAATAATTAATGACCAAAAAATTAGTAGAGGGAATGGTCATTTTATAAGTATAATGGTTAATAATTACAGGACGCa                                          <  1:663762/140‑1 (MQ=255)

                                                                                                tGGACATAAAACACCAAAGAGCGTTGAGATATATCTTTCTG‑AAAAAATATTATTTATAAAATAATTAATGACCAAAAAATTAGTAGAGGGAATGGTCATTTTATAAGTATAATGGTTAATAATTACAGGACGCACTGTgg                                    >  1:690693/1‑140 (MQ=255)

                                                                                                tGGACATAAAACACCAAAGAGCGTTGAGATATATCTTTCTG‑AAAAAATATTATTTATAAAATAATTAATGACCAAAAAATTAGTAGAGGGAATGGTCATTTTATAAGTATAATGGTTAATAATTACAGGACGCACTGTgg                                    >  2:340475/1‑140 (MQ=255)

                                                                                                 ggACATAAAACACCAAAGAGCGTTGAGATATATCTTTCTG‑AAAAAATATTATTTATAAAATAATTAATGACCAAAAAATTAGTAGAGGGAATGGTCATTTTATAAGTATAATGGTTAATAATTACAGGACGCACTGTGGa                                   <  2:519080/140‑1 (MQ=255)

                                                                                                 ggACATAAAACACCAAAGAGCGTTGAGATATATCTTTCTG‑AAAAAATATTATTTATAAAATAATTAATGACCAAAAAATTAGTAGAGGGAATGGTCATTTTATAAGTATAATGGTTAATAATTACAGGACGCACTGTGGa                                   <  1:195827/140‑1 (MQ=255)

                                                                                                   aCATAAAACACCAAAGAGCGTTGAGATATATCTTTCTG‑AAAAAATATTATTTATAAAATAATTAATGACCAAAAAATTAGTAGAGGGAATGGTCATTTTATAAGTATAATGGTTAATAATTACAGGACGCACTGTGGAGt                                 >  1:357265/1‑140 (MQ=255)

                                                                                                   aCATAAAACACCAAAGAGCGTTGAGATATATCTTTCTG‑AAAAAATATTATTTATAAAATAATTAATGACCAAAAAATTAGTAGAGGGAATGGTCATTTTATAAGTATAATGGTTAATAATTACAGGACGCACTGTGGAGt                                 >  1:319198/1‑140 (MQ=255)

                                                                                                      tAAAACACCAAAGAGCGTTGAGATATATCTTTCTG‑AAAAAATATTATTTATAAAATAATTAATGACCAAAAAATTAGTAGAGGGAATGGTCATTTTATAAGTATAATGGTTAATAATTACAGGACGCACTGTGGAGTGGt                              <  1:23926/140‑1 (MQ=255)

                                                                                                           cacCAAAGAGCGTTGAGATATATCTTTCTG‑AAAAAATATTATTTATAAAATAATTAATGACCAAAAAATTAGTAGAGGGAATGGTCATTTTATAAGTATAATGGTTAATAATTACAGGACGCACTGTGGAGTGGTTGata                         <  2:459865/140‑1 (MQ=255)

                                                                                                                               tatCTTTCTG‑AAAAAATATTATTTATAAAATAATTAATGATCAAAAAATTAGTAGAGGGAATGGTCATTTTATAAGTATAATGGTTAATAATTACAGGACGCACTGTGGAGTGGTTGATATAAATCTTAATTTTTTCAAt     >  2:687246/1‑140 (MQ=255)

                                                                                                                               tatCTTTCTG‑AAAAAATATTATTTATAAAATAATTAATGACCAAAAAATTAGTAGAGGGAATGGTCATTTTATAAGTATAATGGTTAATAATTACAGGACGCACTGTGGAGTGGTTGATATAAATCTTAATTTTTTCAAt     >  1:624892/1‑140 (MQ=255)

                                                                                                                                  cTTTCTG‑AAAAAATATTATTTATAAAATAATTAATGACCAAAAAATTAGTAGAGGGAATGGTCATTTTATAAGTATAATGGTTAATAATTACAGGACGCACTGTGGAGTGGTTGATATAAATCTTAATTTTTTCAATGat  <  2:412124/140‑1 (MQ=255)

                                                                                                                                  cTTTCTG‑AAAAAATATTATTTATAAAATAATTAATGACCAAAAAATTAGTAGAGGGAATGGTCATTTTATAAGTATAATGGTTAATAATTACAGGACGCACTGTGGAGTGGTTGATATAAATCTTAATTTTTTCAATGat  <  1:468422/140‑1 (MQ=255)

                                                                                                                                  cTTTCTG‑AAAAAATATTATTTATAAAATAATTAATGACCAAAAAATTAGTAGAGGGAATGGTCATTTTATAAGTATAATGGTTAATAATTACAGGACGCACTGTGGAGTGGTTGATATAAATCTTAATTTTTTCAATGat  <  2:564426/140‑1 (MQ=255)

                                                                                                                                  cTTTCTG‑AAAAAATATTATTTATAAAATAATTAATGACCAAAAAATTAGTAGAGGGAATGGTCATTTTATAAGTATAATGGTTAATAATTACAGGACGCACTGTGGAGTGGTTGATATAAATCTTAATTTTTTCAATGat  <  1:111612/140‑1 (MQ=255)

                                                                                                                                    ttCTG‑AAAAAATATTATTTATAAAATAATTAATGACCAAAAAATTAGTAGAGGGAATGGTCATTTTATAAGTATAATGGTTAATAATTACAGGACGCACTGTGGAGTGGTTGATATAAATCTTAATTTTTTCAATGat  >  2:412464/1‑138 (MQ=255)

                                                                                                                                    ttCTG‑AAAAAATATTATTTATAAAATAATTAATGACCAAAAAATTAGTAGAGGGAATGGTCATTTTATAAGTATAATGGTTAATAATTACAGGACGCACTGTGGAGTGGTTGATATAAATCTTAATTTTTTCAATGat  <  1:412464/138‑1 (MQ=255)

TATTAGAGGCAAACTTGTCATTTTTTTAATTACCCTTTGTTTATTTGTTGTTTACCTTGGGTTTGATAACAATTCAAATTCTGACATCGTATTTTATGGACATAAAACACCAAAGAGCGTTGAGATATATCTTTCTGAAAAAAATATTATTTATAAAATAATTAATGACCAAAAAATTAGTAGAGGGAATGGTCATTTTATAAGTATAATGGTTAATAATTACAGGACGCACTGTGGAGTGGTTGATATAAATCTTAATTTTTTCAATGAT  >  NC_000913/1529933‑1530203

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A