BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504673.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP013494//SRP013494.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 = 91,791,990 number of mapped reads = 91,363,235 (99.53%) number of supplementary alignments = 1,372,855 (1.5%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 45,730,850 number of mapped paired reads (second in pair) = 45,632,385 number of mapped paired reads (both in pair) = 91,222,086 number of mapped paired reads (singletons) = 141,149 number of mapped bases = 9,051,529,051 bp number of sequenced bases = 9,049,237,317 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 42,277,244 duplication rate = 27.98% >>>>>>> Insert size mean insert size = 29,956.7616 std insert size = 1,619,527.7474 median insert size = 146 >>>>>>> Mapping quality mean mapping quality = 53.28 >>>>>>> ACTG content number of A's = 2,694,367,069 bp (29.77%) number of C's = 1,775,781,029 bp (19.62%) number of T's = 2,733,453,100 bp (30.21%) number of G's = 1,773,670,130 bp (19.6%) number of N's = 71,965,989 bp (0.8%) GC percentage = 39.22% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 93,351,463 number of insertions = 965,329 mapped reads with insertion percentage = 1.04% number of deletions = 1,208,692 mapped reads with deletion percentage = 1.3% homopolymer indels = 50.95% >>>>>>> Coverage mean coverageData = 2.9239X std coverageData = 369.8762X There is a 32.66% of reference with a coverageData >= 1X There is a 24.55% of reference with a coverageData >= 2X There is a 17.45% of reference with a coverageData >= 3X There is a 13.97% of reference with a coverageData >= 4X There is a 11.36% of reference with a coverageData >= 5X There is a 9.57% of reference with a coverageData >= 6X There is a 8.18% of reference with a coverageData >= 7X There is a 7.11% of reference with a coverageData >= 8X There is a 6.25% of reference with a coverageData >= 9X There is a 5.55% of reference with a coverageData >= 10X There is a 4.97% of reference with a coverageData >= 11X There is a 4.49% of reference with a coverageData >= 12X There is a 4.07% of reference with a coverageData >= 13X There is a 3.72% of reference with a coverageData >= 14X There is a 3.41% of reference with a coverageData >= 15X There is a 3.14% of reference with a coverageData >= 16X There is a 2.9% of reference with a coverageData >= 17X There is a 2.69% of reference with a coverageData >= 18X There is a 2.51% of reference with a coverageData >= 19X There is a 2.34% of reference with a coverageData >= 20X There is a 2.19% of reference with a coverageData >= 21X There is a 2.06% of reference with a coverageData >= 22X There is a 1.93% of reference with a coverageData >= 23X There is a 1.82% of reference with a coverageData >= 24X There is a 1.72% of reference with a coverageData >= 25X There is a 1.63% of reference with a coverageData >= 26X There is a 1.54% of reference with a coverageData >= 27X There is a 1.46% of reference with a coverageData >= 28X There is a 1.39% of reference with a coverageData >= 29X There is a 1.32% of reference with a coverageData >= 30X There is a 1.26% of reference with a coverageData >= 31X There is a 1.2% of reference with a coverageData >= 32X There is a 1.15% of reference with a coverageData >= 33X There is a 1.1% of reference with a coverageData >= 34X There is a 1.05% of reference with a coverageData >= 35X There is a 1% of reference with a coverageData >= 36X There is a 0.96% of reference with a coverageData >= 37X There is a 0.93% of reference with a coverageData >= 38X There is a 0.89% of reference with a coverageData >= 39X There is a 0.86% of reference with a coverageData >= 40X There is a 0.82% of reference with a coverageData >= 41X There is a 0.79% of reference with a coverageData >= 42X There is a 0.76% of reference with a coverageData >= 43X There is a 0.74% of reference with a coverageData >= 44X There is a 0.71% of reference with a coverageData >= 45X There is a 0.69% of reference with a coverageData >= 46X There is a 0.67% of reference with a coverageData >= 47X There is a 0.64% of reference with a coverageData >= 48X There is a 0.62% of reference with a coverageData >= 49X There is a 0.6% of reference with a coverageData >= 50X There is a 0.58% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 623269347 2.5005728952627164 36.979377557522966 chr2 243199373 633358947 2.604278700175761 14.979032208144188 chr3 198022430 539926439 2.726592330979879 26.474514139737206 chr4 191154276 579562608 3.0319102461511247 49.870152412602124 chr5 180915260 528048379 2.9187608552202837 17.74152759396944 chr6 171115067 502786528 2.9382948960304005 30.17381256512683 chr7 159138663 421584625 2.6491653068619785 14.853986613609615 chr8 146364022 388885134 2.6569721758534346 9.623170774881544 chr9 141213431 396289986 2.80631936490517 35.28117720188654 chr10 135534747 342922586 2.530145173768613 39.909253123837495 chr11 135006516 320138605 2.3712826201662742 14.04811018851419 chr12 133851895 396420102 2.961632347453878 32.34574172356926 chr13 115169878 294571140 2.557709924812111 46.27409126996262 chr14 107349540 238862798 2.225093819684742 15.109525820952864 chr15 102531392 234029783 2.2825183432601794 16.850988606764933 chr16 90354753 178544567 1.976039567060739 9.850358507590384 chr17 81195210 260502829 3.2083521798884442 139.04086428930006 chr18 78077248 194607495 2.4924994154507085 12.578859068589844 chr19 59128983 80238924 1.3570151206558043 6.858180907348108 chr20 63025520 114375601 1.81475061213299 7.204595556982029 chr21 48129895 94333372 1.959974606219274 11.766314493324549 chr22 51304566 45796318 0.8926363006364775 3.4954568234133463 chrMT 16571 3769 0.22744553738458753 1.3968391853893916 chrX 155270560 1634582706 10.52731893283569 1644.2298524927755 chrY 59373566 7886463 0.13282784800225744 1.9196201019723043