BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618618.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 = 31,968,190 number of mapped reads = 31,140,571 (97.41%) number of supplementary alignments = 62,709 (0.2%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,684,130 number of mapped paired reads (second in pair) = 15,456,441 number of mapped paired reads (both in pair) = 30,748,410 number of mapped paired reads (singletons) = 392,161 number of mapped bases = 2,945,879,768 bp number of sequenced bases = 2,943,859,500 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,477,345 duplication rate = 20.91% >>>>>>> Insert size mean insert size = 39,658.2634 std insert size = 1,974,485.0398 median insert size = 194 >>>>>>> Mapping quality mean mapping quality = 53.9496 >>>>>>> ACTG content number of A's = 813,207,291 bp (27.62%) number of C's = 628,770,947 bp (21.36%) number of T's = 823,205,050 bp (27.96%) number of G's = 678,441,286 bp (23.05%) number of N's = 234,926 bp (0.01%) GC percentage = 44.4% >>>>>>> Mismatches and indels general error rate = 0.0116 number of mismatches = 33,306,865 number of insertions = 511,695 mapped reads with insertion percentage = 1.62% number of deletions = 1,506,045 mapped reads with deletion percentage = 4.71% homopolymer indels = 53.57% >>>>>>> Coverage mean coverageData = 0.9516X std coverageData = 3.7607X There is a 20.22% of reference with a coverageData >= 1X There is a 13.56% of reference with a coverageData >= 2X There is a 9.81% of reference with a coverageData >= 3X There is a 7.57% of reference with a coverageData >= 4X There is a 5.99% of reference with a coverageData >= 5X There is a 4.87% of reference with a coverageData >= 6X There is a 4.02% of reference with a coverageData >= 7X There is a 3.37% of reference with a coverageData >= 8X There is a 2.85% of reference with a coverageData >= 9X There is a 2.44% of reference with a coverageData >= 10X There is a 2.1% of reference with a coverageData >= 11X There is a 1.82% of reference with a coverageData >= 12X There is a 1.59% of reference with a coverageData >= 13X There is a 1.4% of reference with a coverageData >= 14X There is a 1.23% of reference with a coverageData >= 15X There is a 1.09% of reference with a coverageData >= 16X There is a 0.97% of reference with a coverageData >= 17X There is a 0.86% of reference with a coverageData >= 18X There is a 0.77% of reference with a coverageData >= 19X There is a 0.69% of reference with a coverageData >= 20X There is a 0.62% of reference with a coverageData >= 21X There is a 0.56% of reference with a coverageData >= 22X There is a 0.5% of reference with a coverageData >= 23X There is a 0.46% of reference with a coverageData >= 24X There is a 0.41% of reference with a coverageData >= 25X There is a 0.38% of reference with a coverageData >= 26X There is a 0.34% of reference with a coverageData >= 27X There is a 0.31% of reference with a coverageData >= 28X There is a 0.29% of reference with a coverageData >= 29X There is a 0.26% of reference with a coverageData >= 30X There is a 0.24% of reference with a coverageData >= 31X There is a 0.22% of reference with a coverageData >= 32X There is a 0.2% of reference with a coverageData >= 33X There is a 0.19% of reference with a coverageData >= 34X There is a 0.17% of reference with a coverageData >= 35X There is a 0.16% of reference with a coverageData >= 36X There is a 0.15% of reference with a coverageData >= 37X There is a 0.14% of reference with a coverageData >= 38X There is a 0.13% of reference with a coverageData >= 39X There is a 0.12% of reference with a coverageData >= 40X There is a 0.11% of reference with a coverageData >= 41X There is a 0.1% of reference with a coverageData >= 42X There is a 0.09% of reference with a coverageData >= 43X There is a 0.09% of reference with a coverageData >= 44X There is a 0.08% of reference with a coverageData >= 45X There is a 0.08% of reference with a coverageData >= 46X There is a 0.07% of reference with a coverageData >= 47X There is a 0.07% of reference with a coverageData >= 48X There is a 0.06% of reference with a coverageData >= 49X There is a 0.06% of reference with a coverageData >= 50X There is a 0.05% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 253431444 1.0167735710475923 4.412862923127292 chr2 243199373 247639643 1.018257736215463 3.8966745479580043 chr3 198022430 189969037 0.959330905089893 3.376932717301464 chr4 191154276 153530904 0.803177973376855 3.175476342125814 chr5 180915260 174861735 0.966539445041839 3.4618656426275978 chr6 171115067 160613028 0.9386258663008326 3.5625108419248654 chr7 159138663 145830468 0.9163735904957301 3.440222617044564 chr8 146364022 149842288 1.0237644876963001 3.6241769757219955 chr9 141213431 129023719 0.9136788058070765 4.15375053918725 chr10 135534747 148849261 1.098236904518662 3.8712799149941652 chr11 135006516 146091347 1.0821058962813321 4.16417897246444 chr12 133851895 134282328 1.0032157408006812 3.6445273121843784 chr13 115169878 77523896 0.6731264923281416 2.708349556697777 chr14 107349540 89790757 0.8364335515550416 3.331464082403242 chr15 102531392 100695645 0.9820957565854563 3.7530868014000953 chr16 90354753 97398390 1.0779553567038138 4.774648985885079 chr17 81195210 92075217 1.133998138560144 4.201938115506309 chr18 78077248 78260983 1.0023532463644211 4.0898491298727295 chr19 59128983 52528085 0.8883644252768562 3.9458025860315913 chr20 63025520 82812649 1.313954236315702 4.523247451595616 chr21 48129895 38171573 0.7930948737785528 4.6150127856629934 chr22 51304566 46726434 0.9107656032018671 3.828853604342709 chrMT 16571 43807 2.6435942308852813 6.591008639778186 chrX 155270560 152121240 0.9797172110411658 3.448714414881988 chrY 59373566 3765890 0.06342704765282246 1.4134371550609164