BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618584.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 = 65,423,242 number of mapped reads = 63,040,982 (96.36%) number of supplementary alignments = 266,349 (0.41%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 31,861,399 number of mapped paired reads (second in pair) = 31,179,583 number of mapped paired reads (both in pair) = 61,736,660 number of mapped paired reads (singletons) = 1,304,322 number of mapped bases = 5,913,227,756 bp number of sequenced bases = 5,909,155,378 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 20,167,883 duplication rate = 26.37% >>>>>>> Insert size mean insert size = 71,418.6244 std insert size = 2,642,298.4094 median insert size = 196 >>>>>>> Mapping quality mean mapping quality = 53.5752 >>>>>>> ACTG content number of A's = 1,623,946,573 bp (27.48%) number of C's = 1,271,738,384 bp (21.52%) number of T's = 1,646,768,282 bp (27.87%) number of G's = 1,366,442,323 bp (23.12%) number of N's = 259,816 bp (0%) GC percentage = 44.65% >>>>>>> Mismatches and indels general error rate = 0.0129 number of mismatches = 74,684,708 number of insertions = 1,081,485 mapped reads with insertion percentage = 1.69% number of deletions = 2,966,687 mapped reads with deletion percentage = 4.59% homopolymer indels = 52.58% >>>>>>> Coverage mean coverageData = 1.9101X std coverageData = 7.6049X There is a 27.92% of reference with a coverageData >= 1X There is a 20.42% of reference with a coverageData >= 2X There is a 15.98% of reference with a coverageData >= 3X There is a 13.12% of reference with a coverageData >= 4X There is a 10.99% of reference with a coverageData >= 5X There is a 9.39% of reference with a coverageData >= 6X There is a 8.11% of reference with a coverageData >= 7X There is a 7.08% of reference with a coverageData >= 8X There is a 6.24% of reference with a coverageData >= 9X There is a 5.53% of reference with a coverageData >= 10X There is a 4.94% of reference with a coverageData >= 11X There is a 4.43% of reference with a coverageData >= 12X There is a 3.99% of reference with a coverageData >= 13X There is a 3.61% of reference with a coverageData >= 14X There is a 3.28% of reference with a coverageData >= 15X There is a 2.98% of reference with a coverageData >= 16X There is a 2.73% of reference with a coverageData >= 17X There is a 2.5% of reference with a coverageData >= 18X There is a 2.29% of reference with a coverageData >= 19X There is a 2.11% of reference with a coverageData >= 20X There is a 1.94% of reference with a coverageData >= 21X There is a 1.8% of reference with a coverageData >= 22X There is a 1.66% of reference with a coverageData >= 23X There is a 1.54% of reference with a coverageData >= 24X There is a 1.43% of reference with a coverageData >= 25X There is a 1.33% of reference with a coverageData >= 26X There is a 1.24% of reference with a coverageData >= 27X There is a 1.15% of reference with a coverageData >= 28X There is a 1.08% of reference with a coverageData >= 29X There is a 1% of reference with a coverageData >= 30X There is a 0.94% of reference with a coverageData >= 31X There is a 0.88% of reference with a coverageData >= 32X There is a 0.82% of reference with a coverageData >= 33X There is a 0.77% of reference with a coverageData >= 34X There is a 0.73% of reference with a coverageData >= 35X There is a 0.68% of reference with a coverageData >= 36X There is a 0.64% of reference with a coverageData >= 37X There is a 0.6% of reference with a coverageData >= 38X There is a 0.57% of reference with a coverageData >= 39X There is a 0.54% of reference with a coverageData >= 40X There is a 0.51% of reference with a coverageData >= 41X There is a 0.48% of reference with a coverageData >= 42X There is a 0.45% of reference with a coverageData >= 43X There is a 0.43% of reference with a coverageData >= 44X There is a 0.41% of reference with a coverageData >= 45X There is a 0.38% of reference with a coverageData >= 46X There is a 0.36% of reference with a coverageData >= 47X There is a 0.34% of reference with a coverageData >= 48X There is a 0.33% of reference with a coverageData >= 49X There is a 0.31% of reference with a coverageData >= 50X There is a 0.29% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 513695719 2.0609606384892416 9.20875947259466 chr2 243199373 498149142 2.048315897590739 9.108088927571952 chr3 198022430 383048851 1.9343710255449345 6.100696538174549 chr4 191154276 308414135 1.6134304785313827 6.035288598626964 chr5 180915260 338748213 1.8724137090480926 6.1515457717871085 chr6 171115067 324928098 1.8988865428197506 6.434627220079851 chr7 159138663 294445596 1.8502455057071832 6.124833419808727 chr8 146364022 292093828 1.9956668586218544 7.119938458799889 chr9 141213431 255072124 1.8062879868700308 7.282027889331851 chr10 135534747 289969064 2.139444462902196 7.003289092565829 chr11 135006516 294645233 2.1824519418010904 7.693440337109594 chr12 133851895 262616811 1.961995465211755 6.720747150892297 chr13 115169878 163783772 1.4221059780926397 5.415851262306438 chr14 107349540 176419715 1.6434137957181745 5.987771342402881 chr15 102531392 189504843 1.8482616816516058 6.941183770570714 chr16 90354753 205160885 2.270615304542972 16.06984458572621 chr17 81195210 189581482 2.334885050485121 8.06064857288405 chr18 78077248 149145394 1.9102286238367419 7.048632533155293 chr19 59128983 120911775 2.044881695326977 8.206438195034117 chr20 63025520 165725270 2.629494687231458 8.129124162528209 chr21 48129895 75201594 1.5624715989926843 8.589695909803668 chr22 51304566 100562964 1.960117234009932 7.581089564351909 chrMT 16571 4673 0.2819986723794581 2.514695354912625 chrX 155270560 312379146 2.0118375692082258 6.386302154905845 chrY 59373566 9019429 0.1519098414941087 5.706325317092047