BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504704.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 = 494,695,710 number of mapped reads = 446,834,233 (90.33%) number of supplementary alignments = 2,283,239 (0.46%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 225,282,406 number of mapped paired reads (second in pair) = 221,551,827 number of mapped paired reads (both in pair) = 439,790,730 number of mapped paired reads (singletons) = 7,043,503 number of mapped bases = 43,888,952,117 bp number of sequenced bases = 43,879,669,166 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 118,150,163 duplication rate = 23.23% >>>>>>> Insert size mean insert size = 43,126.1409 std insert size = 1,940,920.0977 median insert size = 410 >>>>>>> Mapping quality mean mapping quality = 53.7926 >>>>>>> ACTG content number of A's = 11,616,553,312 bp (26.47%) number of C's = 10,218,099,782 bp (23.29%) number of T's = 11,632,311,395 bp (26.51%) number of G's = 10,386,123,611 bp (23.67%) number of N's = 26,581,066 bp (0.06%) GC percentage = 46.96% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 304,560,628 number of insertions = 3,021,793 mapped reads with insertion percentage = 0.66% number of deletions = 3,786,527 mapped reads with deletion percentage = 0.83% homopolymer indels = 41.14% >>>>>>> Coverage mean coverageData = 14.1774X std coverageData = 33.8161X There is a 76% of reference with a coverageData >= 1X There is a 68.26% of reference with a coverageData >= 2X There is a 61.9% of reference with a coverageData >= 3X There is a 56.77% of reference with a coverageData >= 4X There is a 52.3% of reference with a coverageData >= 5X There is a 48.39% of reference with a coverageData >= 6X There is a 44.91% of reference with a coverageData >= 7X There is a 41.79% of reference with a coverageData >= 8X There is a 38.98% of reference with a coverageData >= 9X There is a 36.45% of reference with a coverageData >= 10X There is a 34.14% of reference with a coverageData >= 11X There is a 32.05% of reference with a coverageData >= 12X There is a 30.13% of reference with a coverageData >= 13X There is a 28.38% of reference with a coverageData >= 14X There is a 26.77% of reference with a coverageData >= 15X There is a 25.29% of reference with a coverageData >= 16X There is a 23.92% of reference with a coverageData >= 17X There is a 22.66% of reference with a coverageData >= 18X There is a 21.5% of reference with a coverageData >= 19X There is a 20.42% of reference with a coverageData >= 20X There is a 19.41% of reference with a coverageData >= 21X There is a 18.48% of reference with a coverageData >= 22X There is a 17.6% of reference with a coverageData >= 23X There is a 16.79% of reference with a coverageData >= 24X There is a 16.03% of reference with a coverageData >= 25X There is a 15.32% of reference with a coverageData >= 26X There is a 14.65% of reference with a coverageData >= 27X There is a 14.02% of reference with a coverageData >= 28X There is a 13.43% of reference with a coverageData >= 29X There is a 12.88% of reference with a coverageData >= 30X There is a 12.36% of reference with a coverageData >= 31X There is a 11.87% of reference with a coverageData >= 32X There is a 11.4% of reference with a coverageData >= 33X There is a 10.96% of reference with a coverageData >= 34X There is a 10.55% of reference with a coverageData >= 35X There is a 10.15% of reference with a coverageData >= 36X There is a 9.78% of reference with a coverageData >= 37X There is a 9.42% of reference with a coverageData >= 38X There is a 9.09% of reference with a coverageData >= 39X There is a 8.77% of reference with a coverageData >= 40X There is a 8.46% of reference with a coverageData >= 41X There is a 8.17% of reference with a coverageData >= 42X There is a 7.9% of reference with a coverageData >= 43X There is a 7.63% of reference with a coverageData >= 44X There is a 7.38% of reference with a coverageData >= 45X There is a 7.14% of reference with a coverageData >= 46X There is a 6.91% of reference with a coverageData >= 47X There is a 6.69% of reference with a coverageData >= 48X There is a 6.48% of reference with a coverageData >= 49X There is a 6.28% of reference with a coverageData >= 50X There is a 6.09% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3615970742 14.507369038811742 30.9850517159598 chr2 243199373 2996738657 12.322147956360068 23.670431185707503 chr3 198022430 2555552443 12.905368563551109 24.600363675201177 chr4 191154276 1881060120 9.840533831427344 17.696681275301433 chr5 180915260 2865202931 15.837265087533247 30.72258996147258 chr6 171115067 1324499403 7.740401977576878 15.520440040017744 chr7 159138663 2248126164 14.126838328407974 24.388393910254425 chr8 146364022 2463864595 16.83381312792839 33.26107719325398 chr9 141213431 1051265988 7.444518418364893 27.747380416002226 chr10 135534747 2983361959 22.011786829837813 35.309775894894244 chr11 135006516 2632170206 19.49661604481372 35.76990810423437 chr12 133851895 1997143687 14.920548468887946 35.35603466274968 chr13 115169878 612736082 5.320280724791599 10.80668706189594 chr14 107349540 1267049839 11.80302998037998 23.371787838872905 chr15 102531392 1558593186 15.201131630008495 29.791178962248136 chr16 90354753 2208851656 24.44643566232758 41.263600314928695 chr17 81195210 1720656079 21.19159589586627 40.29838811359263 chr18 78077248 682660436 8.743397769347608 97.12096171354821 chr19 59128983 1893224064 32.01854603181658 59.7909813361615 chr20 63025520 1352961426 21.466882399383614 35.08827742030498 chr21 48129895 560690016 11.649516708897869 25.109764077883707 chr22 51304566 724918999 14.129717011932232 29.31348880849664 chrMT 16571 193266 11.662905075131253 17.846791322638893 chrX 155270560 2609375913 16.805348760254358 28.171708088484518 chrY 59373566 82084260 1.3825051370503836 47.806177338657946