BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2976561.sorted.bam outfile = /home/yangyx/scDNA/SRP067062/SRP067062.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 = 530,130,538 number of mapped reads = 511,163,888 (96.42%) number of supplementary alignments = 5,264,665 (0.99%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 259,216,119 number of mapped paired reads (second in pair) = 251,947,769 number of mapped paired reads (both in pair) = 501,965,782 number of mapped paired reads (singletons) = 9,198,106 number of mapped bases = 103,500,161,378 bp number of sequenced bases = 103,449,185,203 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 98,173,916 duplication rate = 11.22% >>>>>>> Insert size mean insert size = 37,027.505 std insert size = 1,729,625.7384 median insert size = 588 >>>>>>> Mapping quality mean mapping quality = 54.5075 >>>>>>> ACTG content number of A's = 31,183,288,984 bp (30.14%) number of C's = 20,728,214,818 bp (20.04%) number of T's = 31,170,161,790 bp (30.13%) number of G's = 20,288,228,001 bp (19.61%) number of N's = 79,291,610 bp (0.08%) GC percentage = 39.65% >>>>>>> Mismatches and indels general error rate = 0.0216 number of mismatches = 2,186,888,584 number of insertions = 15,486,861 mapped reads with insertion percentage = 2.7% number of deletions = 17,116,166 mapped reads with deletion percentage = 3.06% homopolymer indels = 40.53% >>>>>>> Coverage mean coverageData = 33.4336X std coverageData = 616.5514X There is a 92.37% of reference with a coverageData >= 1X There is a 92.34% of reference with a coverageData >= 2X There is a 92.31% of reference with a coverageData >= 3X There is a 92.28% of reference with a coverageData >= 4X There is a 92.23% of reference with a coverageData >= 5X There is a 92.17% of reference with a coverageData >= 6X There is a 92.09% of reference with a coverageData >= 7X There is a 91.97% of reference with a coverageData >= 8X There is a 91.81% of reference with a coverageData >= 9X There is a 91.59% of reference with a coverageData >= 10X There is a 91.31% of reference with a coverageData >= 11X There is a 90.94% of reference with a coverageData >= 12X There is a 90.48% of reference with a coverageData >= 13X There is a 89.92% of reference with a coverageData >= 14X There is a 89.25% of reference with a coverageData >= 15X There is a 88.46% of reference with a coverageData >= 16X There is a 87.54% of reference with a coverageData >= 17X There is a 86.49% of reference with a coverageData >= 18X There is a 85.29% of reference with a coverageData >= 19X There is a 83.93% of reference with a coverageData >= 20X There is a 82.41% of reference with a coverageData >= 21X There is a 80.7% of reference with a coverageData >= 22X There is a 78.8% of reference with a coverageData >= 23X There is a 76.68% of reference with a coverageData >= 24X There is a 74.35% of reference with a coverageData >= 25X There is a 71.8% of reference with a coverageData >= 26X There is a 69.03% of reference with a coverageData >= 27X There is a 66.04% of reference with a coverageData >= 28X There is a 62.87% of reference with a coverageData >= 29X There is a 59.52% of reference with a coverageData >= 30X There is a 56.03% of reference with a coverageData >= 31X There is a 52.44% of reference with a coverageData >= 32X There is a 48.79% of reference with a coverageData >= 33X There is a 45.11% of reference with a coverageData >= 34X There is a 41.45% of reference with a coverageData >= 35X There is a 37.84% of reference with a coverageData >= 36X There is a 34.33% of reference with a coverageData >= 37X There is a 30.95% of reference with a coverageData >= 38X There is a 27.72% of reference with a coverageData >= 39X There is a 24.68% of reference with a coverageData >= 40X There is a 21.83% of reference with a coverageData >= 41X There is a 19.2% of reference with a coverageData >= 42X There is a 16.79% of reference with a coverageData >= 43X There is a 14.59% of reference with a coverageData >= 44X There is a 12.61% of reference with a coverageData >= 45X There is a 10.85% of reference with a coverageData >= 46X There is a 9.28% of reference with a coverageData >= 47X There is a 7.91% of reference with a coverageData >= 48X There is a 6.72% of reference with a coverageData >= 49X There is a 5.68% of reference with a coverageData >= 50X There is a 4.79% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 8355564390 33.52274251705877 1336.781963224161 chr2 243199373 8931066207 36.72322875190965 294.4777102440063 chr3 198022430 6789264448 34.285330444637005 23.802699901716817 chr4 191154276 7385918080 38.638518763765454 488.96563984100953 chr5 180915260 6303232906 34.84080284880336 34.27401580698029 chr6 171115067 5971427780 34.89714777717382 193.1180950215575 chr7 159138663 5708969042 35.8741800036362 511.6454138076857 chr8 146364022 5504601178 37.6089772799493 1017.9262091721768 chr9 141213431 4682357380 33.15801724270831 1162.9965276162561 chr10 135534747 5633948929 41.568299301137884 1056.4515583846082 chr11 135006516 4742701733 35.12942836773893 284.116657455909 chr12 133851895 4455038121 33.28333992581876 23.163401691183015 chr13 115169878 3434086077 29.817571544184496 17.3027892218716 chr14 107349540 3081918142 28.709188153018633 24.841761788561392 chr15 102531392 2749879359 26.8198773600967 19.007276433672182 chr16 90354753 3219668576 35.63363817728548 335.7576771570991 chr17 81195210 2697378649 33.2209085856173 314.3503086256522 chr18 78077248 3110374227 39.837139585145216 727.5016857410983 chr19 59128983 1938627911 32.78642406212195 674.8099494088654 chr20 63025520 2051579574 32.55156917388385 213.00307448682537 chr21 48129895 1549866063 32.2017337249541 288.46610431209496 chr22 51304566 1139637312 22.213175178209283 94.74677195318561 chrMT 16571 78726871 4750.882324542876 896.7147672711719 chrX 155270560 2816222456 18.13751722155185 46.67235563231748 chrY 59373566 1168105967 19.673838809008036 528.6393072291122