BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618628.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 37,266,812 number of mapped reads = 33,510,406 (89.92%) number of supplementary alignments = 61,878 (0.17%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 17,058,277 number of mapped paired reads (second in pair) = 16,452,129 number of mapped paired reads (both in pair) = 32,219,394 number of mapped paired reads (singletons) = 1,291,012 number of mapped bases = 3,148,037,249 bp number of sequenced bases = 3,146,115,822 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 22,009,365 duplication rate = 45.93% >>>>>>> Insert size mean insert size = 63,277.7775 std insert size = 2,583,853.3314 median insert size = 203 >>>>>>> Mapping quality mean mapping quality = 52.8921 >>>>>>> ACTG content number of A's = 784,513,976 bp (24.94%) number of C's = 769,593,379 bp (24.46%) number of T's = 792,660,981 bp (25.19%) number of G's = 796,752,040 bp (25.32%) number of N's = 2,595,446 bp (0.08%) GC percentage = 49.79% >>>>>>> Mismatches and indels general error rate = 0.0149 number of mismatches = 45,960,498 number of insertions = 560,514 mapped reads with insertion percentage = 1.65% number of deletions = 1,398,955 mapped reads with deletion percentage = 4.08% homopolymer indels = 51.74% >>>>>>> Coverage mean coverageData = 1.0169X std coverageData = 5.947X There is a 11.86% of reference with a coverageData >= 1X There is a 8.67% of reference with a coverageData >= 2X There is a 6.95% of reference with a coverageData >= 3X There is a 5.9% of reference with a coverageData >= 4X There is a 5.08% of reference with a coverageData >= 5X There is a 4.48% of reference with a coverageData >= 6X There is a 3.98% of reference with a coverageData >= 7X There is a 3.58% of reference with a coverageData >= 8X There is a 3.23% of reference with a coverageData >= 9X There is a 2.94% of reference with a coverageData >= 10X There is a 2.68% of reference with a coverageData >= 11X There is a 2.46% of reference with a coverageData >= 12X There is a 2.26% of reference with a coverageData >= 13X There is a 2.09% of reference with a coverageData >= 14X There is a 1.93% of reference with a coverageData >= 15X There is a 1.79% of reference with a coverageData >= 16X There is a 1.66% of reference with a coverageData >= 17X There is a 1.54% of reference with a coverageData >= 18X There is a 1.44% of reference with a coverageData >= 19X There is a 1.34% of reference with a coverageData >= 20X There is a 1.26% of reference with a coverageData >= 21X There is a 1.18% of reference with a coverageData >= 22X There is a 1.11% of reference with a coverageData >= 23X There is a 1.04% of reference with a coverageData >= 24X There is a 0.98% of reference with a coverageData >= 25X There is a 0.92% of reference with a coverageData >= 26X There is a 0.87% of reference with a coverageData >= 27X There is a 0.82% of reference with a coverageData >= 28X There is a 0.77% of reference with a coverageData >= 29X There is a 0.73% of reference with a coverageData >= 30X There is a 0.69% of reference with a coverageData >= 31X There is a 0.65% of reference with a coverageData >= 32X There is a 0.61% of reference with a coverageData >= 33X There is a 0.58% of reference with a coverageData >= 34X There is a 0.55% of reference with a coverageData >= 35X There is a 0.52% of reference with a coverageData >= 36X There is a 0.49% of reference with a coverageData >= 37X There is a 0.47% of reference with a coverageData >= 38X There is a 0.44% of reference with a coverageData >= 39X There is a 0.42% of reference with a coverageData >= 40X There is a 0.4% of reference with a coverageData >= 41X There is a 0.38% of reference with a coverageData >= 42X There is a 0.36% of reference with a coverageData >= 43X There is a 0.35% of reference with a coverageData >= 44X There is a 0.33% of reference with a coverageData >= 45X There is a 0.32% of reference with a coverageData >= 46X There is a 0.3% of reference with a coverageData >= 47X There is a 0.29% of reference with a coverageData >= 48X There is a 0.28% of reference with a coverageData >= 49X There is a 0.26% of reference with a coverageData >= 50X There is a 0.25% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 297407797 1.1932078476145502 6.827441202401313 chr2 243199373 262548218 1.079559600673806 6.168322433131763 chr3 198022430 186241424 0.940506709265208 5.376507252840767 chr4 191154276 128113034 0.6702075238955156 4.651995128840525 chr5 180915260 160434764 0.886795088485073 5.048695670468829 chr6 171115067 150152438 0.8774939614172024 4.913220965181372 chr7 159138663 158058634 0.9932132834369735 5.4806018871083 chr8 146364022 145007228 0.9907300033064137 5.415283579837229 chr9 141213431 143268739 1.0145546212243792 6.417975307072666 chr10 135534747 167448334 1.2354642459324472 6.292278849953788 chr11 135006516 180027942 1.3334759486719885 7.012481432890611 chr12 133851895 144540065 1.0798507185871369 5.843861227225836 chr13 115169878 73087171 0.634603181571487 3.989131043853391 chr14 107349540 104658084 0.9749281086812296 5.867430495660973 chr15 102531392 116038776 1.131739009258745 6.224650857258299 chr16 90354753 136428984 1.5099259249815005 8.18634957821085 chr17 81195210 147397328 1.8153451170333816 8.175826688135382 chr18 78077248 73866481 0.9460692185257349 5.246244283837944 chr19 59128983 106231507 1.7966063613845684 8.61450664780791 chr20 63025520 108072676 1.7147446938954252 7.743279834272006 chr21 48129895 40113019 0.8334325059300461 6.943742580406543 chr22 51304566 89069495 1.736092943462381 8.358436065650375 chrMT 16571 6221 0.37541488141934704 3.0580798343749613 chrX 155270560 5691794 0.03665726458383353 0.8478780634033432 chrY 59373566 24127096 0.4063609047837888 3.691223845936648