BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514713.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 85,186,229 number of mapped reads = 84,420,512 (99.1%) number of supplementary alignments = 4,209,659 (4.94%) number of secondary alignments = 0 number of mapped bases = 8,102,563,069 bp number of sequenced bases = 8,095,351,651 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 50,895,775 duplication rate = 38.93% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.4652 >>>>>>> ACTG content number of A's = 2,404,089,605 bp (29.7%) number of C's = 1,652,086,432 bp (20.41%) number of T's = 2,361,682,601 bp (29.17%) number of G's = 1,675,630,246 bp (20.7%) number of N's = 1,862,767 bp (0.02%) GC percentage = 41.11% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 50,042,095 number of insertions = 2,774,680 mapped reads with insertion percentage = 3.14% number of deletions = 2,844,160 mapped reads with deletion percentage = 3.15% homopolymer indels = 41.49% >>>>>>> Coverage mean coverageData = 2.6174X std coverageData = 127.3414X There is a 12.11% of reference with a coverageData >= 1X There is a 8.41% of reference with a coverageData >= 2X There is a 6.75% of reference with a coverageData >= 3X There is a 5.84% of reference with a coverageData >= 4X There is a 5.21% of reference with a coverageData >= 5X There is a 4.75% of reference with a coverageData >= 6X There is a 4.39% of reference with a coverageData >= 7X There is a 4.1% of reference with a coverageData >= 8X There is a 3.86% of reference with a coverageData >= 9X There is a 3.65% of reference with a coverageData >= 10X There is a 3.47% of reference with a coverageData >= 11X There is a 3.3% of reference with a coverageData >= 12X There is a 3.16% of reference with a coverageData >= 13X There is a 3.02% of reference with a coverageData >= 14X There is a 2.9% of reference with a coverageData >= 15X There is a 2.79% of reference with a coverageData >= 16X There is a 2.69% of reference with a coverageData >= 17X There is a 2.59% of reference with a coverageData >= 18X There is a 2.51% of reference with a coverageData >= 19X There is a 2.42% of reference with a coverageData >= 20X There is a 2.35% of reference with a coverageData >= 21X There is a 2.27% of reference with a coverageData >= 22X There is a 2.2% of reference with a coverageData >= 23X There is a 2.14% of reference with a coverageData >= 24X There is a 2.08% of reference with a coverageData >= 25X There is a 2.02% of reference with a coverageData >= 26X There is a 1.96% of reference with a coverageData >= 27X There is a 1.91% of reference with a coverageData >= 28X There is a 1.86% of reference with a coverageData >= 29X There is a 1.81% of reference with a coverageData >= 30X There is a 1.76% of reference with a coverageData >= 31X There is a 1.72% of reference with a coverageData >= 32X There is a 1.68% of reference with a coverageData >= 33X There is a 1.64% of reference with a coverageData >= 34X There is a 1.6% of reference with a coverageData >= 35X There is a 1.56% of reference with a coverageData >= 36X There is a 1.52% of reference with a coverageData >= 37X There is a 1.49% of reference with a coverageData >= 38X There is a 1.45% of reference with a coverageData >= 39X There is a 1.42% of reference with a coverageData >= 40X There is a 1.39% of reference with a coverageData >= 41X There is a 1.36% of reference with a coverageData >= 42X There is a 1.33% of reference with a coverageData >= 43X There is a 1.3% of reference with a coverageData >= 44X There is a 1.28% of reference with a coverageData >= 45X There is a 1.25% of reference with a coverageData >= 46X There is a 1.23% of reference with a coverageData >= 47X There is a 1.2% of reference with a coverageData >= 48X There is a 1.18% of reference with a coverageData >= 49X There is a 1.15% of reference with a coverageData >= 50X There is a 1.13% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 655215921 2.6287433843544967 37.87065767511861 chr2 243199373 695951530 2.861650181968191 26.763052260147568 chr3 198022430 398014405 2.0099460702507286 20.64411836505812 chr4 191154276 620816614 3.247725486402407 30.290936051952556 chr5 180915260 386339135 2.1354701366816706 26.51738618848183 chr6 171115067 585020385 3.4188712616405663 322.8487821773085 chr7 159138663 637444354 4.005590734415056 34.798708256916065 chr8 146364022 530792965 3.6265262306060433 37.05072633262045 chr9 141213431 248631911 1.7606817512988548 20.806134007293142 chr10 135534747 470269789 3.46973598585756 28.627456333325508 chr11 135006516 313086519 2.3190474673089114 25.545921740598466 chr12 133851895 232978920 1.7405724438940517 37.56330053973756 chr13 115169878 303665798 2.636677256877879 21.80522564190574 chr14 107349540 157753961 1.469535509886675 16.550311371117814 chr15 102531392 184961838 1.803953251702659 21.323076466945775 chr16 90354753 216785687 2.399272642580297 51.0058087887943 chr17 81195210 136069951 1.6758371706902415 31.015966951927084 chr18 78077248 155309179 1.989173324858991 20.81628295724983 chr19 59128983 275138016 4.653183634157888 591.3870162883442 chr20 63025520 241379068 3.8298623795567255 81.2090112301047 chr21 48129895 63660957 1.322690543995577 89.65947161522745 chr22 51304566 220267780 4.293336776301743 407.30790300749936 chrMT 16571 5452526 329.0402510409752 191.13466337043803 chrX 155270560 341072869 2.1966357885229497 27.998230615014435 chrY 59373566 26482991 0.44604009467782346 8.621839628169043