BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5365341.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP102259/SRP102259.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 = 103,530,222 number of mapped reads = 100,991,294 (97.55%) number of supplementary alignments = 801,143 (0.77%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 50,723,193 number of mapped paired reads (second in pair) = 50,268,101 number of mapped paired reads (both in pair) = 100,381,830 number of mapped paired reads (singletons) = 609,464 number of mapped bases = 13,499,557,971 bp number of sequenced bases = 13,494,165,367 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 41,906,652 duplication rate = 28.14% >>>>>>> Insert size mean insert size = 64,431.9964 std insert size = 2,487,796.534 median insert size = 213 >>>>>>> Mapping quality mean mapping quality = 54.2284 >>>>>>> ACTG content number of A's = 4,051,911,854 bp (30.03%) number of C's = 2,654,991,968 bp (19.68%) number of T's = 4,009,791,906 bp (29.72%) number of G's = 2,776,972,010 bp (20.58%) number of N's = 497,629 bp (0%) GC percentage = 40.25% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 102,119,030 number of insertions = 4,314,208 mapped reads with insertion percentage = 4.13% number of deletions = 2,194,870 mapped reads with deletion percentage = 2.1% homopolymer indels = 49.96% >>>>>>> Coverage mean coverageData = 4.3608X std coverageData = 56.3406X There is a 71.91% of reference with a coverageData >= 1X There is a 62.62% of reference with a coverageData >= 2X There is a 52.2% of reference with a coverageData >= 3X There is a 44.04% of reference with a coverageData >= 4X There is a 36.1% of reference with a coverageData >= 5X There is a 29.77% of reference with a coverageData >= 6X There is a 24.05% of reference with a coverageData >= 7X There is a 19.52% of reference with a coverageData >= 8X There is a 15.6% of reference with a coverageData >= 9X There is a 12.52% of reference with a coverageData >= 10X There is a 9.93% of reference with a coverageData >= 11X There is a 7.91% of reference with a coverageData >= 12X There is a 6.24% of reference with a coverageData >= 13X There is a 4.96% of reference with a coverageData >= 14X There is a 3.91% of reference with a coverageData >= 15X There is a 3.1% of reference with a coverageData >= 16X There is a 2.44% of reference with a coverageData >= 17X There is a 1.94% of reference with a coverageData >= 18X There is a 1.54% of reference with a coverageData >= 19X There is a 1.23% of reference with a coverageData >= 20X There is a 0.98% of reference with a coverageData >= 21X There is a 0.79% of reference with a coverageData >= 22X There is a 0.64% of reference with a coverageData >= 23X There is a 0.52% of reference with a coverageData >= 24X There is a 0.43% of reference with a coverageData >= 25X There is a 0.36% of reference with a coverageData >= 26X There is a 0.3% of reference with a coverageData >= 27X There is a 0.25% of reference with a coverageData >= 28X There is a 0.22% of reference with a coverageData >= 29X There is a 0.19% of reference with a coverageData >= 30X There is a 0.16% of reference with a coverageData >= 31X There is a 0.14% of reference with a coverageData >= 32X There is a 0.13% of reference with a coverageData >= 33X There is a 0.11% of reference with a coverageData >= 34X There is a 0.1% of reference with a coverageData >= 35X There is a 0.09% of reference with a coverageData >= 36X There is a 0.09% of reference with a coverageData >= 37X There is a 0.08% of reference with a coverageData >= 38X There is a 0.07% of reference with a coverageData >= 39X There is a 0.07% of reference with a coverageData >= 40X There is a 0.07% of reference with a coverageData >= 41X There is a 0.06% of reference with a coverageData >= 42X There is a 0.06% of reference with a coverageData >= 43X There is a 0.06% of reference with a coverageData >= 44X There is a 0.05% of reference with a coverageData >= 45X There is a 0.05% of reference with a coverageData >= 46X There is a 0.05% of reference with a coverageData >= 47X There is a 0.05% of reference with a coverageData >= 48X There is a 0.05% of reference with a coverageData >= 49X There is a 0.04% of reference with a coverageData >= 50X There is a 0.04% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1115288103 4.47456499215703 154.77824603639743 chr2 243199373 1180761467 4.855117233382012 31.038584570636257 chr3 198022430 930543134 4.699180461526505 6.396033663901853 chr4 191154276 932393037 4.877699084272643 25.125086643773617 chr5 180915260 853444214 4.717369966469384 6.1602431600700776 chr6 171115067 801908471 4.686369733882055 22.78130545872283 chr7 159138663 745143851 4.682355858425177 40.331915006961935 chr8 146364022 704154684 4.810982059511866 19.512228439825524 chr9 141213431 573298180 4.059799241050945 55.513218910904904 chr10 135534747 707407055 5.2193778396915445 107.39808393859566 chr11 135006516 630360961 4.669115089230211 33.984784105245915 chr12 133851895 610641376 4.562067470169175 23.115968707797226 chr13 115169878 449524113 3.9031396125990514 4.716050330788242 chr14 107349540 416031017 3.87548020233715 5.284632016266075 chr15 102531392 370776526 3.6162244437293896 11.055809375258987 chr16 90354753 374817042 4.148282514811368 16.827560160036743 chr17 81195210 361018467 4.446302522033012 28.31847772968857 chr18 78077248 389062636 4.983047507002296 54.58654894784808 chr19 59128983 242440248 4.100193098196869 78.16053831849986 chr20 63025520 268180229 4.255105376361829 9.91077887021582 chr21 48129895 192609354 4.001865244044268 18.85595079771315 chr22 51304566 150597446 2.9353614647086186 16.314051877432256 chrMT 16571 15087270 910.4622533341379 221.60930965377463 chrX 155270560 366377260 2.3596054525725934 11.254228781821523 chrY 59373566 117691830 1.9822260633629452 36.91152189196159