BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818973.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 2,635,520 number of mapped reads = 2,391,780 (90.75%) number of supplementary alignments = 33,889 (1.29%) number of secondary alignments = 0 number of mapped bases = 221,655,261 bp number of sequenced bases = 221,529,780 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,179,732 duplication rate = 42.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.1322 >>>>>>> ACTG content number of A's = 65,965,393 bp (29.78%) number of C's = 44,853,922 bp (20.25%) number of T's = 63,448,296 bp (28.64%) number of G's = 47,251,401 bp (21.33%) number of N's = 10,768 bp (0%) GC percentage = 41.58% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 1,353,049 number of insertions = 33,113 mapped reads with insertion percentage = 1.35% number of deletions = 69,353 mapped reads with deletion percentage = 2.84% homopolymer indels = 42.51% >>>>>>> Coverage mean coverageData = 0.0716X std coverageData = 0.8045X There is a 2.98% of reference with a coverageData >= 1X There is a 1.61% of reference with a coverageData >= 2X There is a 0.95% of reference with a coverageData >= 3X There is a 0.57% of reference with a coverageData >= 4X There is a 0.34% of reference with a coverageData >= 5X There is a 0.21% of reference with a coverageData >= 6X There is a 0.13% of reference with a coverageData >= 7X There is a 0.08% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% 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 22005778 0.08828775596109749 1.4040155894826665 chr2 243199373 17649027 0.07257019943057172 1.0536112576708045 chr3 198022430 13453400 0.06793876835063584 0.5053107741622587 chr4 191154276 12139600 0.06350681896333828 0.5485778629805078 chr5 180915260 11935656 0.06597373820207317 0.5122935856922645 chr6 171115067 9394397 0.0549010508817438 0.55006738851332 chr7 159138663 10910607 0.06856037869314008 0.9754498503886859 chr8 146364022 20284026 0.13858614789910598 0.8296224455950596 chr9 141213431 9441783 0.06686179163793562 0.7858937164336296 chr10 135534747 11277701 0.08320892796590383 0.9365476330102701 chr11 135006516 7422648 0.05497992408010884 0.5418414232614647 chr12 133851895 10305989 0.07699546577207592 0.5646081820195941 chr13 115169878 4742032 0.04117423828477095 0.39112953864373445 chr14 107349540 5282960 0.04921269341256609 0.45412721670355577 chr15 102531392 5766782 0.05624406230630322 0.46235972981864665 chr16 90354753 6883321 0.07618106155411658 0.8663441335577536 chr17 81195210 7498109 0.09234669138733677 0.6610881755237775 chr18 78077248 5278560 0.06760689106255384 0.919338192455201 chr19 59128983 4412658 0.07462766609735196 1.3655479721625592 chr20 63025520 6224020 0.09875396506050248 0.646398786706226 chr21 48129895 3095748 0.06432068883590958 0.5309568710564434 chr22 51304566 1733098 0.03378058007546541 0.38074755300885876 chrMT 16571 37340 2.2533341379518435 2.8933275157025227 chrX 155270560 13702383 0.08824842906472419 0.6757125222392529 chrY 59373566 777638 0.013097377374975254 0.7478116219713082