BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153389.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 92,024,220 number of mapped reads = 91,344,817 (99.26%) number of supplementary alignments = 477,824 (0.52%) number of secondary alignments = 0 number of mapped bases = 8,788,412,134 bp number of sequenced bases = 8,787,476,094 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 58,941,818 duplication rate = 49.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.0667 >>>>>>> ACTG content number of A's = 2,169,811,488 bp (24.69%) number of C's = 2,223,183,486 bp (25.3%) number of T's = 2,158,090,111 bp (24.56%) number of G's = 2,235,225,110 bp (25.44%) number of N's = 1,165,899 bp (0.01%) GC percentage = 50.74% >>>>>>> Mismatches and indels general error rate = 0.0029 number of mismatches = 24,411,687 number of insertions = 614,852 mapped reads with insertion percentage = 0.66% number of deletions = 397,981 mapped reads with deletion percentage = 0.43% homopolymer indels = 44.69% >>>>>>> Coverage mean coverageData = 2.8389X std coverageData = 43.8131X There is a 8.45% of reference with a coverageData >= 1X There is a 5.86% of reference with a coverageData >= 2X There is a 4.11% of reference with a coverageData >= 3X There is a 3.63% of reference with a coverageData >= 4X There is a 3.21% of reference with a coverageData >= 5X There is a 2.99% of reference with a coverageData >= 6X There is a 2.8% of reference with a coverageData >= 7X There is a 2.66% of reference with a coverageData >= 8X There is a 2.53% of reference with a coverageData >= 9X There is a 2.43% of reference with a coverageData >= 10X There is a 2.34% of reference with a coverageData >= 11X There is a 2.25% of reference with a coverageData >= 12X There is a 2.18% of reference with a coverageData >= 13X There is a 2.11% of reference with a coverageData >= 14X There is a 2.05% of reference with a coverageData >= 15X There is a 1.99% of reference with a coverageData >= 16X There is a 1.94% of reference with a coverageData >= 17X There is a 1.89% of reference with a coverageData >= 18X There is a 1.84% of reference with a coverageData >= 19X There is a 1.8% of reference with a coverageData >= 20X There is a 1.75% of reference with a coverageData >= 21X There is a 1.71% of reference with a coverageData >= 22X There is a 1.68% of reference with a coverageData >= 23X There is a 1.64% of reference with a coverageData >= 24X There is a 1.61% of reference with a coverageData >= 25X There is a 1.57% of reference with a coverageData >= 26X There is a 1.54% of reference with a coverageData >= 27X There is a 1.51% of reference with a coverageData >= 28X There is a 1.49% of reference with a coverageData >= 29X There is a 1.46% of reference with a coverageData >= 30X There is a 1.43% of reference with a coverageData >= 31X There is a 1.41% of reference with a coverageData >= 32X There is a 1.38% of reference with a coverageData >= 33X There is a 1.36% of reference with a coverageData >= 34X There is a 1.34% of reference with a coverageData >= 35X There is a 1.31% of reference with a coverageData >= 36X There is a 1.29% of reference with a coverageData >= 37X There is a 1.27% of reference with a coverageData >= 38X There is a 1.25% of reference with a coverageData >= 39X There is a 1.23% of reference with a coverageData >= 40X There is a 1.21% of reference with a coverageData >= 41X There is a 1.2% of reference with a coverageData >= 42X There is a 1.18% of reference with a coverageData >= 43X There is a 1.16% of reference with a coverageData >= 44X There is a 1.15% of reference with a coverageData >= 45X There is a 1.13% of reference with a coverageData >= 46X There is a 1.11% of reference with a coverageData >= 47X There is a 1.1% of reference with a coverageData >= 48X There is a 1.08% of reference with a coverageData >= 49X There is a 1.07% of reference with a coverageData >= 50X There is a 1.05% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1082191247 4.341779541644552 56.3579136070028 chr2 243199373 537999139 2.2121732155945977 31.60874437977182 chr3 198022430 118262097 0.5972156639023165 14.229146498155112 chr4 191154276 261008191 1.3654321339900344 31.763963717254338 chr5 180915260 96590627 0.5338998324408897 13.065722726403038 chr6 171115067 521473231 3.047500375872804 40.271009377335304 chr7 159138663 602044535 3.783144357571987 61.81835308428148 chr8 146364022 430610950 2.9420546396299496 53.0237459228777 chr9 141213431 476747894 3.3760803814758953 46.07307564740228 chr10 135534747 476026443 3.512209625477074 50.20112836492172 chr11 135006516 512359123 3.795069587604201 49.677886219897495 chr12 133851895 360782574 2.6953863746195004 40.410240873853674 chr13 115169878 196271818 1.7041940254551629 31.672610016222734 chr14 107349540 259240922 2.414923454725563 32.41800818736769 chr15 102531392 530365496 5.1727133091102475 61.38184899797527 chr16 90354753 352849839 3.905160794363524 42.55617074718804 chr17 81195210 446272180 5.496287034666207 58.81801998715559 chr18 78077248 151208898 1.9366576291213542 28.730574815917027 chr19 59128983 413425366 6.991924180397285 70.65385039407407 chr20 63025520 148726824 2.3597873369390685 47.136721927718554 chr21 48129895 82372326 1.711458668255977 34.493945868927554 chr22 51304566 209944864 4.0921282522885 70.40318775856286 chrMT 16571 2261 0.13644318387544505 0.5503166978032691 chrX 155270560 511368825 3.2934049120451423 41.818339832401556 chrY 59373566 10266464 0.17291304349144196 9.416660189981151