BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006064.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 11,153,122 number of mapped reads = 9,713,119 (87.09%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,932,429 number of mapped paired reads (second in pair) = 4,780,690 number of mapped paired reads (both in pair) = 8,872,630 number of mapped paired reads (singletons) = 840,489 number of mapped bases = 374,915,004 bp number of sequenced bases = 374,871,086 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 564,049 duplication rate = 5.2% >>>>>>> Insert size mean insert size = 58,882.686 std insert size = 2,360,991.1095 median insert size = 105 >>>>>>> Mapping quality mean mapping quality = 47.4344 >>>>>>> ACTG content number of A's = 103,113,779 bp (27.51%) number of C's = 80,737,313 bp (21.54%) number of T's = 106,252,142 bp (28.34%) number of G's = 84,752,752 bp (22.61%) number of N's = 15,100 bp (0%) GC percentage = 44.15% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 1,922,318 number of insertions = 13,041 mapped reads with insertion percentage = 0.13% number of deletions = 34,854 mapped reads with deletion percentage = 0.36% homopolymer indels = 45.65% >>>>>>> Coverage mean coverageData = 0.1211X std coverageData = 0.6234X There is a 7.34% of reference with a coverageData >= 1X There is a 2.83% of reference with a coverageData >= 2X There is a 1.08% of reference with a coverageData >= 3X There is a 0.43% of reference with a coverageData >= 4X There is a 0.18% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 31885951 0.1279272680327645 0.7001650323171982 chr2 243199373 32097575 0.13198050062407027 0.6783274658223616 chr3 198022430 25670612 0.12963487015082079 0.5328052729497199 chr4 191154276 23343151 0.12211681312323874 0.5380277433842564 chr5 180915260 22929063 0.12673924244975243 0.5296794178294032 chr6 171115067 21973957 0.12841626038693602 0.6101739617853527 chr7 159138663 20892017 0.13128184318099995 0.8325269431453878 chr8 146364022 18538373 0.12665935758447525 0.6747080649231488 chr9 141213431 16261050 0.11515229029454005 0.5771520486371523 chr10 135534747 18060449 0.1332532756341811 0.5690739407594564 chr11 135006516 17621801 0.13052555922560063 0.9409989732119199 chr12 133851895 17495087 0.1307048137047294 0.5427992378732188 chr13 115169878 11648429 0.1011412810561456 0.4755897749926317 chr14 107349540 11848864 0.11037647669473014 0.5166994912659163 chr15 102531392 11343935 0.11063865201400952 0.5028443952288361 chr16 90354753 11682428 0.12929511300860952 0.5884663713143106 chr17 81195210 11091191 0.13659908016741382 0.6340467164129644 chr18 78077248 9771921 0.12515708801621697 0.8093163347342729 chr19 59128983 7952592 0.13449566687118567 0.7462188330772032 chr20 63025520 8695669 0.13797060301922143 0.5625320821146839 chr21 48129895 5067693 0.1052920019875381 0.5450697892394719 chr22 51304566 5052214 0.09847493885826848 0.5224094026248742 chrMT 16571 55266 3.335103494055881 4.907872525921822 chrX 155270560 11509485 0.07412535254590438 0.4440809211459578 chrY 59373566 2426231 0.040863824820628086 0.34526252258296275