BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779339.sorted.bam outfile = /home/yangyx/scDNA/SRP052954/SRP052954.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 161,009,040 number of mapped reads = 155,638,903 (96.66%) number of supplementary alignments = 880,094 (0.55%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 78,464,376 number of mapped paired reads (second in pair) = 77,174,527 number of mapped paired reads (both in pair) = 153,454,526 number of mapped paired reads (singletons) = 2,184,377 number of mapped bases = 15,398,801,811 bp number of sequenced bases = 15,395,328,518 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,565,205 duplication rate = 7.13% >>>>>>> Insert size mean insert size = 59,928.4497 std insert size = 2,403,804.1684 median insert size = 187 >>>>>>> Mapping quality mean mapping quality = 53.7932 >>>>>>> ACTG content number of A's = 4,569,721,353 bp (29.68%) number of C's = 3,118,856,885 bp (20.26%) number of T's = 4,544,328,430 bp (29.52%) number of G's = 3,161,590,575 bp (20.54%) number of N's = 831,275 bp (0.01%) GC percentage = 40.79% >>>>>>> Mismatches and indels general error rate = 0.0039 number of mismatches = 57,828,558 number of insertions = 1,549,087 mapped reads with insertion percentage = 0.98% number of deletions = 1,575,513 mapped reads with deletion percentage = 0.99% homopolymer indels = 47.06% >>>>>>> Coverage mean coverageData = 4.9743X std coverageData = 7.886X There is a 82.38% of reference with a coverageData >= 1X There is a 71.53% of reference with a coverageData >= 2X There is a 60.17% of reference with a coverageData >= 3X There is a 49.77% of reference with a coverageData >= 4X There is a 40.75% of reference with a coverageData >= 5X There is a 33.2% of reference with a coverageData >= 6X There is a 27.01% of reference with a coverageData >= 7X There is a 21.98% of reference with a coverageData >= 8X There is a 17.93% of reference with a coverageData >= 9X There is a 14.67% of reference with a coverageData >= 10X There is a 12.04% of reference with a coverageData >= 11X There is a 9.93% of reference with a coverageData >= 12X There is a 8.22% of reference with a coverageData >= 13X There is a 6.83% of reference with a coverageData >= 14X There is a 5.7% of reference with a coverageData >= 15X There is a 4.78% of reference with a coverageData >= 16X There is a 4.02% of reference with a coverageData >= 17X There is a 3.39% of reference with a coverageData >= 18X There is a 2.88% of reference with a coverageData >= 19X There is a 2.45% of reference with a coverageData >= 20X There is a 2.09% of reference with a coverageData >= 21X There is a 1.79% of reference with a coverageData >= 22X There is a 1.54% of reference with a coverageData >= 23X There is a 1.33% of reference with a coverageData >= 24X There is a 1.15% of reference with a coverageData >= 25X There is a 0.99% of reference with a coverageData >= 26X There is a 0.86% of reference with a coverageData >= 27X There is a 0.75% of reference with a coverageData >= 28X There is a 0.66% of reference with a coverageData >= 29X There is a 0.58% of reference with a coverageData >= 30X There is a 0.51% of reference with a coverageData >= 31X There is a 0.45% of reference with a coverageData >= 32X There is a 0.39% of reference with a coverageData >= 33X There is a 0.35% of reference with a coverageData >= 34X There is a 0.31% of reference with a coverageData >= 35X There is a 0.28% of reference with a coverageData >= 36X There is a 0.25% of reference with a coverageData >= 37X There is a 0.22% of reference with a coverageData >= 38X There is a 0.2% of reference with a coverageData >= 39X There is a 0.18% of reference with a coverageData >= 40X There is a 0.16% of reference with a coverageData >= 41X There is a 0.14% of reference with a coverageData >= 42X There is a 0.13% of reference with a coverageData >= 43X There is a 0.12% of reference with a coverageData >= 44X There is a 0.11% of reference with a coverageData >= 45X There is a 0.1% of reference with a coverageData >= 46X There is a 0.09% of reference with a coverageData >= 47X There is a 0.08% of reference with a coverageData >= 48X There is a 0.07% of reference with a coverageData >= 49X There is a 0.07% of reference with a coverageData >= 50X There is a 0.06% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1235676898 4.95756798134517 8.720436550573924 chr2 243199373 1285200077 5.284553414535324 18.259563129371525 chr3 198022430 1063922767 5.372738669048753 5.446483940157164 chr4 191154276 993803052 5.198957997675135 5.752889224232847 chr5 180915260 937561669 5.182324968054105 5.244113115067192 chr6 171115067 919752898 5.375055009036697 6.066424031444918 chr7 159138663 807243446 5.0725790375654976 5.970043207863324 chr8 146364022 797288040 5.447295237623355 5.681293993990026 chr9 141213431 628121768 4.448031349086051 6.36571713060362 chr10 135534747 875278196 6.457961632525127 7.7148383199153265 chr11 135006516 733949163 5.436398069853162 5.831356920261651 chr12 133851895 712043572 5.319637588993417 5.9294158007759385 chr13 115169878 511023706 4.437129871753446 5.190223580200991 chr14 107349540 472702247 4.403393316822783 5.384302088695078 chr15 102531392 415801400 4.055357016902687 5.005750849148889 chr16 90354753 374213144 4.1415988819094 5.411363854547424 chr17 81195210 361189856 4.448413348521421 6.134562295200729 chr18 78077248 385259074 4.934332137321234 6.208694230655885 chr19 59128983 248238594 4.198255769087048 6.379211281120387 chr20 63025520 313319308 4.9713085746853025 5.798766109560737 chr21 48129895 179973181 3.7393221198591853 7.176977989154052 chr22 51304566 150154411 2.9267260734648843 4.480729784081229 chrMT 16571 783666 47.291412708949366 13.057821702048036 chrX 155270560 979831437 6.310477897419833 6.628354827140763 chrY 59373566 16470241 0.277400232285189 2.8196403085348876