BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2093991.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 383,566 number of mapped reads = 364,053 (94.91%) number of supplementary alignments = 21,359 (5.57%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 183,015 number of mapped paired reads (second in pair) = 181,038 number of mapped paired reads (both in pair) = 360,716 number of mapped paired reads (singletons) = 3,337 number of mapped bases = 46,802,736 bp number of sequenced bases = 45,992,558 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 344,175 duplication rate = 50.59% >>>>>>> Insert size mean insert size = 975,688.678 std insert size = 8,926,681.5508 median insert size = 164 >>>>>>> Mapping quality mean mapping quality = 41.3699 >>>>>>> ACTG content number of A's = 12,035,124 bp (26.17%) number of C's = 10,894,699 bp (23.69%) number of T's = 11,399,995 bp (24.79%) number of G's = 11,662,343 bp (25.36%) number of N's = 397 bp (0%) GC percentage = 49.04% >>>>>>> Mismatches and indels general error rate = 0.0342 number of mismatches = 1,520,740 number of insertions = 24,267 mapped reads with insertion percentage = 6.54% number of deletions = 122,841 mapped reads with deletion percentage = 32.41% homopolymer indels = 30.75% >>>>>>> Coverage mean coverageData = 0.0151X std coverageData = 3.139X There is a 0.02% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% 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 687163 0.002756915899519464 0.9104846231369496 chr2 243199373 2246264 0.009236306707090072 2.909247999295651 chr3 198022430 978889 0.0049433238446775956 1.7971652577033141 chr4 191154276 1222101 0.006393270532959462 2.1114262462931808 chr5 180915260 475297 0.0026271802610791373 1.2622614472076976 chr6 171115067 900640 0.005263358836776191 1.606869282235783 chr7 159138663 819230 0.00514790048223542 1.3977360962001781 chr8 146364022 619373 0.004231729844100622 1.3843796651842661 chr9 141213431 672826 0.004764603446254344 1.5541211248362965 chr10 135534747 678709 0.005007638373353809 1.4240544346287367 chr11 135006516 947908 0.007021201850731412 1.955638051763605 chr12 133851895 1067200 0.007972991342408713 1.7983934565275068 chr13 115169878 1013658 0.008801415939678255 2.524718671278973 chr14 107349540 156377 0.0014567086174752124 0.46053730736853 chr15 102531392 719822 0.007020503535151459 1.9076497694073873 chr16 90354753 246733 0.0027307141219233924 0.6881799464062407 chr17 81195210 1251660 0.015415441378869518 3.878830565551376 chr18 78077248 248812 0.0031867414179352223 0.8530222875255683 chr19 59128983 171314 0.0028972931937625243 0.7932760435250517 chr20 63025520 461226 0.007318083214545473 2.678821121648953 chr21 48129895 107484 0.0022332066172178434 0.3955143460376606 chr22 51304566 165961 0.0032348192946413386 0.979272793129138 chrMT 16571 2110706 127.37348379699475 536.0494361280133 chrX 155270560 28079555 0.1808427495849825 10.018244816481296 chrY 59373566 753828 0.012696357163388164 2.026553715126602