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
A8 F1 I2 R1	765	53.2	2691310	93.4%	2513683	103.8

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,815,820	A→G	intergenic (‑52/+14)	pyrE ← / ← rph	orotate phosphoribosyltransferase/ribonuclease PH (defective),enzyme, Degradation of RNA, RNase PH

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,815,820	0	A	G	97.6%	143.4 / ‑5.3	42	intergenic (‑52/+14)	pyrE/rph	orotate phosphoribosyltransferase/ribonuclease PH (defective),enzyme, Degradation of RNA, RNase PH
Reads supporting (aligned to +/- strand): ref base A (0/1); new base G (20/21); total (20/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

GCCCGGATTTCAGCGTAAACTCGCCAAACTTTAACACCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCC  >  NC_000913/3815684‑3815947

gcCCGGATTTCAGCGTAAACTCGCCAAACTTTAACACCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCGGt                                                                                                                               <  2:712160/139‑1 (MQ=255)

                aaaCTCGCCAAACTTTAACACCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCGGTCGCCTTAAAAATCAGt                                                                                                               >  1:609147/1‑139 (MQ=255)

                    tCGCCAAACTTTAACACCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCGGTCGCCTTAAAAATCAGTTTGc                                                                                                           <  2:377663/139‑1 (MQ=255)

                           aCTTTAACACCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCGGTCGCCTTAAAAATCAGTTTGCCAgcgca                                                                                                    >  2:386299/1‑138 (MQ=255)

                                    ccTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCGGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGc                                                                                           <  2:609147/139‑1 (MQ=255)

                                                           aTAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCGGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGgatt                                                                           >  2:1087347/1‑132 (MQ=255)

                                                           aTAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCGGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGgatt                                                                           <  1:1087347/132‑1 (MQ=255)

                                                                   gcgcTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCGGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGc                                                            >  2:871349/1‑139 (MQ=255)

                                                                   gcgcTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCGGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGc                                                            <  2:714498/139‑1 (MQ=255)

                                                                    cgcTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCGGTCGCCTTAAAAATCAGTTTGCCAgcg                                                                                                      <  2:954372/96‑1 (MQ=255)

                                                                    cgcTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCGGTCGCCTTAAAAATCAGTTTGCCAgcg                                                                                                      >  1:954372/1‑96 (MQ=255)

                                                                       tGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCGGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCaga                                                        <  2:945088/139‑1 (MQ=255)

                                                                          tatGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCGGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGcc                                                     <  2:945851/139‑1 (MQ=255)

                                                                                ttCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCGGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAg                                               <  2:555050/139‑1 (MQ=255)

                                                                                   aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCGGTCGCCTTAAAAATCAGTTTGCCAgcg                                                                                                      >  1:210289/1‑81 (MQ=255)

                                                                                   aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCGGTCGCCTTAAAAATCAGTTTGCCAgcg                                                                                                      <  2:210289/81‑1 (MQ=255)

                                                                                   aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCGGTCGCCTTAAAAATCAGTTTGCCAgc                                                                                                       >  2:1163742/1‑80 (MQ=255)

                                                                                   aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCGGTCGCCTTAAAAATCAGTTTGCCAgc                                                                                                       <  1:1163742/80‑1 (MQ=255)

                                                                                   aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCGGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGgattcga                                                                        >  1:436950/1‑111 (MQ=255)

                                                                                   aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCGGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGgattcga                                                                        <  2:436950/111‑1 (MQ=255)

                                                                                   aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCGGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATg                                            >  1:936674/1‑139 (MQ=255)

                                                                                       cTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCGGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTa                                        >  1:97913/1‑139 (MQ=255)

                                                                                          cGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCAACTCATCGGTCGCATTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGct                                     >  1:908061/1‑139 (MQ=255)

                                                                                                       aCTTTTCTACAGACAAAAAAAAGGCGACTCATCGGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCt                                                                 >  1:620316/1‑98 (MQ=255)

                                                                                                       aCTTTTCTACAGACAAAAAAAAGGCGACTCATCGGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCt                                                                 <  2:620316/98‑1 (MQ=255)

                                                                                                         ttttCTACAGACAAAAAAAAGGCGACTCATCGGTCGCCTTAAAAATCAGTTTGCCa                                                                                                         <  1:797617/56‑1 (MQ=255)

                                                                                                         ttttCTACAGACAAAAAAAAGGCGACTCATCGGTCGCCTTAAAAATCAGTTTGCCa                                                                                                         >  2:797617/1‑56 (MQ=255)

                                                                                                           ttCTACAGACAAAAAAAAGGCGACTCATCGGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGc                                                            <  1:126/99‑1 (MQ=255)

                                                                                                           ttCTACAGACAAAAAAAAGGCGACTCATCGGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGc                                                            >  2:126/1‑99 (MQ=255)

                                                                                                            tCTACAGACAAAAAAAAGGCGACTCATCGGTCGCCt                                                                                                                          >  1:305904/1‑36 (MQ=255)

                                                                                                            tCTACAGACAAAAAAAAGGCGACTCATCGGTCGCCt                                                                                                                          <  2:305904/36‑1 (MQ=255)

                                                                                                              tACAGACAAAAAAAAGGCGACTCATCGGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGt                                                                                         >  1:739030/1‑67 (MQ=255)

                                                                                                              tACAGACAAAAAAAAGGCGACTCATCGGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGt                                                                                         <  2:739030/67‑1 (MQ=255)

                                                                                                              tACAGACAAAAAAAAGGCGACTCATCGGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCg                 >  2:727095/1‑139 (MQ=255)

                                                                                                                cAGACAAAAAAAAGGCGACTCATCGGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGcc               <  2:936674/139‑1 (MQ=255)

                                                                                                                cAGAC‑AAAAAAAGGCGACTCATCGGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGt                                                                                         <  2:544000/64‑1 (MQ=255)

                                                                                                                cAGAC‑AAAAAAAGGCGACTCATCGGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGt                                                                                         >  1:544000/1‑64 (MQ=255)

                                                                                                                             ggCGACTCATCGGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCt                                                                 >  1:442420/1‑76 (MQ=255)

                                                                                                                             ggCGACTCATCGGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCt                                                                 <  2:442420/76‑1 (MQ=255)

                                                                                                                             ggCGACTCATCGGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGc                    >  2:1303855/1‑121 (MQ=255)

                                                                                                                             ggCGACTCATCGGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGc                    <  1:1303855/121‑1 (MQ=255)

                                                                                                                             ggCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTcccc  <  1:871349/139‑1 (MQ=255)

GCCCGGATTTCAGCGTAAACTCGCCAAACTTTAACACCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCC  >  NC_000913/3815684‑3815947

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A