BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779381.sorted.bam outfile = /home/yangyx/scDNA/SRP052627/SRP052627.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 = 15,171,528 number of mapped reads = 14,334,968 (94.49%) number of supplementary alignments = 57,862 (0.38%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,244,122 number of mapped paired reads (second in pair) = 7,090,846 number of mapped paired reads (both in pair) = 14,151,204 number of mapped paired reads (singletons) = 183,764 number of mapped bases = 1,139,144,089 bp number of sequenced bases = 1,138,894,235 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 727,908 duplication rate = 4.73% >>>>>>> Insert size mean insert size = 38,038.8094 std insert size = 1,836,516.6887 median insert size = 178 >>>>>>> Mapping quality mean mapping quality = 52.6603 >>>>>>> ACTG content number of A's = 343,066,059 bp (30.12%) number of C's = 224,905,832 bp (19.75%) number of T's = 342,459,820 bp (30.07%) number of G's = 228,209,958 bp (20.04%) number of N's = 252,566 bp (0.02%) GC percentage = 39.79% >>>>>>> Mismatches and indels general error rate = 0.0035 number of mismatches = 3,788,014 number of insertions = 100,732 mapped reads with insertion percentage = 0.7% number of deletions = 119,807 mapped reads with deletion percentage = 0.83% homopolymer indels = 47.14% >>>>>>> Coverage mean coverageData = 0.368X std coverageData = 1.7621X There is a 13.16% of reference with a coverageData >= 1X There is a 7.11% of reference with a coverageData >= 2X There is a 4.34% of reference with a coverageData >= 3X There is a 2.9% of reference with a coverageData >= 4X There is a 2.04% of reference with a coverageData >= 5X There is a 1.49% of reference with a coverageData >= 6X There is a 1.11% of reference with a coverageData >= 7X There is a 0.84% of reference with a coverageData >= 8X There is a 0.65% of reference with a coverageData >= 9X There is a 0.51% of reference with a coverageData >= 10X There is a 0.41% of reference with a coverageData >= 11X There is a 0.33% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.22% of reference with a coverageData >= 14X There is a 0.18% of reference with a coverageData >= 15X There is a 0.15% of reference with a coverageData >= 16X There is a 0.13% of reference with a coverageData >= 17X There is a 0.11% of reference with a coverageData >= 18X There is a 0.09% of reference with a coverageData >= 19X There is a 0.08% of reference with a coverageData >= 20X There is a 0.07% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 89679707 0.3597973262421681 3.0938654172782774 chr2 243199373 92603665 0.38077263052812227 1.4807501302644306 chr3 198022430 69359582 0.3502612406079453 1.470026638946385 chr4 191154276 82751982 0.43290677944342715 1.5159832905423454 chr5 180915260 87316688 0.4826386010776537 1.6798008537066325 chr6 171115067 50131119 0.2929672990163981 1.6292609902089035 chr7 159138663 108044258 0.6789315428646023 2.15004551207591 chr8 146364022 64058292 0.4376641959183111 1.681534839150609 chr9 141213431 81380325 0.5762930935372571 2.8854433713237397 chr10 135534747 38074088 0.28091754212666953 1.23482849387346 chr11 135006516 26947422 0.19960089926326222 0.9267738235020213 chr12 133851895 65548869 0.4897119237646953 1.6464078926375174 chr13 115169878 54276538 0.47127373009807305 1.4757473474472156 chr14 107349540 16440820 0.15315221658145903 0.8539932970394261 chr15 102531392 27234671 0.2656227567845758 1.1293286972318908 chr16 90354753 20809775 0.23031190179890149 1.0842337890641824 chr17 81195210 8982473 0.11062811463878226 0.8091282729990723 chr18 78077248 62730117 0.8034365786048197 2.3821567585743866 chr19 59128983 20100001 0.33993483365002236 2.152154419191062 chr20 63025520 32005893 0.507824338458453 1.7927159264686765 chr21 48129895 8658007 0.17988834174684984 0.8046974253450314 chr22 51304566 8705176 0.1696764377657926 1.0408995421070715 chrMT 16571 411 0.02480236557842013 0.15552237215312315 chrX 155270560 15347177 0.09884151251853539 0.8425339263987216 chrY 59373566 7957033 0.1340164240766674 0.7425947387908641