BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779302.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 = 18,970,532 number of mapped reads = 18,226,877 (96.08%) number of supplementary alignments = 46,060 (0.24%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,184,069 number of mapped paired reads (second in pair) = 9,042,808 number of mapped paired reads (both in pair) = 18,056,066 number of mapped paired reads (singletons) = 170,811 number of mapped bases = 1,451,042,549 bp number of sequenced bases = 1,450,765,136 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 499,781 duplication rate = 2.55% >>>>>>> Insert size mean insert size = 42,605.2771 std insert size = 1,932,147.3005 median insert size = 212 >>>>>>> Mapping quality mean mapping quality = 52.7062 >>>>>>> ACTG content number of A's = 446,365,513 bp (30.77%) number of C's = 276,904,673 bp (19.09%) number of T's = 446,026,792 bp (30.74%) number of G's = 281,078,975 bp (19.37%) number of N's = 389,183 bp (0.03%) GC percentage = 38.46% >>>>>>> Mismatches and indels general error rate = 0.0036 number of mismatches = 5,043,329 number of insertions = 104,961 mapped reads with insertion percentage = 0.57% number of deletions = 133,653 mapped reads with deletion percentage = 0.72% homopolymer indels = 46.54% >>>>>>> Coverage mean coverageData = 0.4687X std coverageData = 1.506X There is a 20.5% of reference with a coverageData >= 1X There is a 9.9% of reference with a coverageData >= 2X There is a 5.5% of reference with a coverageData >= 3X There is a 3.34% of reference with a coverageData >= 4X There is a 2.14% of reference with a coverageData >= 5X There is a 1.43% of reference with a coverageData >= 6X There is a 0.99% of reference with a coverageData >= 7X There is a 0.7% of reference with a coverageData >= 8X There is a 0.5% of reference with a coverageData >= 9X There is a 0.37% of reference with a coverageData >= 10X There is a 0.28% of reference with a coverageData >= 11X There is a 0.21% of reference with a coverageData >= 12X There is a 0.16% of reference with a coverageData >= 13X There is a 0.13% of reference with a coverageData >= 14X There is a 0.1% of reference with a coverageData >= 15X There is a 0.08% of reference with a coverageData >= 16X There is a 0.07% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% 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% 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 121969625 0.48934532042750656 1.8350256732988695 chr2 243199373 114978512 0.47277470571439345 1.33571636156091 chr3 198022430 103333091 0.5218251841470686 1.4088766564908461 chr4 191154276 124543936 0.6515362282557572 1.5206045266672772 chr5 180915260 85048515 0.47010138890439646 1.2986659712266724 chr6 171115067 96990167 0.566812547255117 1.5312517383351483 chr7 159138663 121885243 0.7659059131343839 2.495154626347758 chr8 146364022 110201067 0.7529245609279581 1.7425318472766684 chr9 141213431 50556898 0.3580176307733788 1.1894876970693846 chr10 135534747 33349363 0.24605766224656767 1.8176594017184098 chr11 135006516 55663241 0.4123004033375693 1.261237177937879 chr12 133851895 57140034 0.42688998911819664 1.3078622380351277 chr13 115169878 54904391 0.47672526839005597 1.3197741088108261 chr14 107349540 45037019 0.4195362085389467 1.2807846192463912 chr15 102531392 37296837 0.36376017405479094 1.1603551210884346 chr16 90354753 23646773 0.2617103385806389 0.9529099683422133 chr17 81195210 17577798 0.2164881154935125 0.8728783082440508 chr18 78077248 35407883 0.4534980920434081 1.416186521291755 chr19 59128983 11744861 0.19863120256947425 1.061227604585638 chr20 63025520 24003020 0.38084604458638344 1.2016685753898546 chr21 48129895 15140321 0.31457207625323097 1.0167171606718663 chr22 51304566 6410658 0.12495297202202237 0.5864281205947166 chrMT 16571 580 0.03500090519582403 0.19306976032221973 chrX 155270560 103191824 0.6645936228992798 1.8860308406866886 chrY 59373566 1020892 0.01719438579788184 0.22004211148783145