BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779089.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 = 28,083,946 number of mapped reads = 27,115,386 (96.55%) number of supplementary alignments = 205,304 (0.73%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 13,739,200 number of mapped paired reads (second in pair) = 13,376,186 number of mapped paired reads (both in pair) = 26,650,094 number of mapped paired reads (singletons) = 465,292 number of mapped bases = 2,706,564,790 bp number of sequenced bases = 2,705,864,168 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 801,420 duplication rate = 2.21% >>>>>>> Insert size mean insert size = 70,421.3906 std insert size = 2,549,215.1426 median insert size = 286 >>>>>>> Mapping quality mean mapping quality = 53.8396 >>>>>>> ACTG content number of A's = 813,851,489 bp (30.08%) number of C's = 534,838,218 bp (19.77%) number of T's = 810,669,812 bp (29.96%) number of G's = 545,602,663 bp (20.16%) number of N's = 901,986 bp (0.03%) GC percentage = 39.93% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 15,029,851 number of insertions = 273,923 mapped reads with insertion percentage = 1% number of deletions = 315,882 mapped reads with deletion percentage = 1.14% homopolymer indels = 47.21% >>>>>>> Coverage mean coverageData = 0.8743X std coverageData = 3.3082X There is a 40.95% of reference with a coverageData >= 1X There is a 20.87% of reference with a coverageData >= 2X There is a 10.77% of reference with a coverageData >= 3X There is a 5.63% of reference with a coverageData >= 4X There is a 3% of reference with a coverageData >= 5X There is a 1.63% of reference with a coverageData >= 6X There is a 0.91% of reference with a coverageData >= 7X There is a 0.53% of reference with a coverageData >= 8X There is a 0.32% of reference with a coverageData >= 9X There is a 0.2% of reference with a coverageData >= 10X There is a 0.14% of reference with a coverageData >= 11X There is a 0.1% of reference with a coverageData >= 12X There is a 0.08% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.04% 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 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% 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 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.03% of reference with a coverageData >= 36X There is a 0.03% of reference with a coverageData >= 37X There is a 0.03% of reference with a coverageData >= 38X There is a 0.03% of reference with a coverageData >= 39X There is a 0.03% of reference with a coverageData >= 40X There is a 0.03% of reference with a coverageData >= 41X There is a 0.03% of reference with a coverageData >= 42X There is a 0.03% of reference with a coverageData >= 43X There is a 0.03% of reference with a coverageData >= 44X There is a 0.03% of reference with a coverageData >= 45X There is a 0.03% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 241618243 0.9693787001638002 8.171613076155582 chr2 243199373 180014564 0.740193372126827 1.9075582716206747 chr3 198022430 170376785 0.8603913455662573 1.3915296831382604 chr4 191154276 172701082 0.9034643933364065 1.443115191859656 chr5 180915260 171250157 0.9465766293014751 1.471410592435645 chr6 171115067 143130743 0.8364590302267187 1.6987737858843004 chr7 159138663 264101203 1.659566556745547 6.1948838872162355 chr8 146364022 195853829 1.3381282252547009 1.9364736537722007 chr9 141213431 100689755 0.713032423948399 2.089290910950265 chr10 135534747 74452495 0.5493240416053604 3.782060877217528 chr11 135006516 123024710 0.9112501651401774 1.6900980501454859 chr12 133851895 113013884 0.8443203885906883 1.4925092400779805 chr13 115169878 90929834 0.7895279180551011 1.4055097658988085 chr14 107349540 74499489 0.6939898298586096 1.305480102388196 chr15 102531392 66314511 0.6467727561915867 1.3345470996357311 chr16 90354753 57719363 0.6388082650173367 1.3247837941061027 chr17 81195210 63515735 0.7822596308329026 3.5562559640119096 chr18 78077248 85993759 1.1013933149897905 2.4344676033670543 chr19 59128983 41979680 0.7099679018663317 4.986250998660601 chr20 63025520 68645472 1.0891694665906764 1.7033639505973384 chr21 48129895 35274323 0.7328983992173679 1.416374517254951 chr22 51304566 26932288 0.5249491439027084 1.165038682491316 chrMT 16571 5202 0.31392191177358036 0.623643454020543 chrX 155270560 142490729 0.9176931480120893 1.7648996705336044 chrY 59373566 2036955 0.03430743910513982 0.5167648874520091