BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1781849.sorted.bam outfile = /home/yangyx/scDNA/SRP052954/SRP052954.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 = 157,371,624 number of mapped reads = 153,893,276 (97.79%) number of supplementary alignments = 402,256 (0.26%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 77,590,219 number of mapped paired reads (second in pair) = 76,303,057 number of mapped paired reads (both in pair) = 152,154,314 number of mapped paired reads (singletons) = 1,738,962 number of mapped bases = 15,298,732,275 bp number of sequenced bases = 15,295,641,749 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,574,612 duplication rate = 6.6% >>>>>>> Insert size mean insert size = 24,433.8529 std insert size = 1,487,048.2984 median insert size = 210 >>>>>>> Mapping quality mean mapping quality = 54.0135 >>>>>>> ACTG content number of A's = 4,552,455,316 bp (29.76%) number of C's = 3,081,534,061 bp (20.15%) number of T's = 4,539,910,195 bp (29.68%) number of G's = 3,120,010,808 bp (20.4%) number of N's = 1,731,369 bp (0.01%) GC percentage = 40.54% >>>>>>> Mismatches and indels general error rate = 0.004 number of mismatches = 57,557,774 number of insertions = 1,701,187 mapped reads with insertion percentage = 1.09% number of deletions = 1,382,660 mapped reads with deletion percentage = 0.88% homopolymer indels = 47.2% >>>>>>> Coverage mean coverageData = 4.9419X std coverageData = 6.6281X There is a 79.99% of reference with a coverageData >= 1X There is a 68.27% of reference with a coverageData >= 2X There is a 57.11% of reference with a coverageData >= 3X There is a 47.27% of reference with a coverageData >= 4X There is a 38.92% of reference with a coverageData >= 5X There is a 31.98% of reference with a coverageData >= 6X There is a 26.31% of reference with a coverageData >= 7X There is a 21.69% of reference with a coverageData >= 8X There is a 17.94% of reference with a coverageData >= 9X There is a 14.89% of reference with a coverageData >= 10X There is a 12.42% of reference with a coverageData >= 11X There is a 10.4% of reference with a coverageData >= 12X There is a 8.75% of reference with a coverageData >= 13X There is a 7.39% of reference with a coverageData >= 14X There is a 6.27% of reference with a coverageData >= 15X There is a 5.34% of reference with a coverageData >= 16X There is a 4.57% of reference with a coverageData >= 17X There is a 3.92% of reference with a coverageData >= 18X There is a 3.38% of reference with a coverageData >= 19X There is a 2.93% of reference with a coverageData >= 20X There is a 2.54% of reference with a coverageData >= 21X There is a 2.21% of reference with a coverageData >= 22X There is a 1.93% of reference with a coverageData >= 23X There is a 1.69% of reference with a coverageData >= 24X There is a 1.49% of reference with a coverageData >= 25X There is a 1.31% of reference with a coverageData >= 26X There is a 1.16% of reference with a coverageData >= 27X There is a 1.03% of reference with a coverageData >= 28X There is a 0.91% of reference with a coverageData >= 29X There is a 0.81% of reference with a coverageData >= 30X There is a 0.73% of reference with a coverageData >= 31X There is a 0.65% of reference with a coverageData >= 32X There is a 0.58% of reference with a coverageData >= 33X There is a 0.53% of reference with a coverageData >= 34X There is a 0.47% of reference with a coverageData >= 35X There is a 0.43% of reference with a coverageData >= 36X There is a 0.39% of reference with a coverageData >= 37X There is a 0.35% of reference with a coverageData >= 38X There is a 0.32% of reference with a coverageData >= 39X There is a 0.29% of reference with a coverageData >= 40X There is a 0.27% of reference with a coverageData >= 41X There is a 0.24% of reference with a coverageData >= 42X There is a 0.22% of reference with a coverageData >= 43X There is a 0.2% of reference with a coverageData >= 44X There is a 0.19% of reference with a coverageData >= 45X There is a 0.17% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.14% of reference with a coverageData >= 49X There is a 0.13% of reference with a coverageData >= 50X There is a 0.12% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1274073667 5.111616821207439 7.92766170042486 chr2 243199373 712510966 2.929740143696834 5.878305466863693 chr3 198022430 1112263098 5.616854100820801 6.048972354582545 chr4 191154276 1050814926 5.497208579315275 5.961236740830901 chr5 180915260 983492094 5.436203082039625 5.712175361361939 chr6 171115067 965121602 5.6401906560338135 6.320630599336968 chr7 159138663 835419519 5.24963263641344 6.667102371542596 chr8 146364022 801878941 5.478661559327742 5.877980672006073 chr9 141213431 650376917 4.605630727859023 6.634894691129354 chr10 135534747 869110395 6.412454475603957 9.254817522732836 chr11 135006516 741503382 5.492352546894848 6.2942735914931776 chr12 133851895 1067918604 7.97835999258733 8.378394616539712 chr13 115169878 504981305 4.384664755831381 5.409419426369936 chr14 107349540 467116646 4.3513614124475986 5.542602450795796 chr15 102531392 434886927 4.241500271448572 5.680017288967016 chr16 90354753 360553353 3.99041933079049 5.516630655792111 chr17 81195210 323413980 3.9831657557139146 5.3740509057516155 chr18 78077248 207059404 2.651981330079667 4.44008820614319 chr19 59128983 207297192 3.5058474115815588 5.850563801134357 chr20 63025520 297479031 4.7199774154977225 6.344972705923513 chr21 48129895 187860458 3.9031969215806517 7.098488311113038 chr22 51304566 131855649 2.570056805470297 4.5160423865179595 chrMT 16571 848071 51.17802184539255 17.55953736239041 chrX 155270560 1097086803 7.065645947306431 7.7373893360955615 chrY 59373566 13809345 0.23258405937753512 2.5772534826878393