BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779428.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 = 19,777,076 number of mapped reads = 18,076,672 (91.4%) number of supplementary alignments = 224,249 (1.13%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,089,310 number of mapped paired reads (second in pair) = 8,987,362 number of mapped paired reads (both in pair) = 17,897,480 number of mapped paired reads (singletons) = 179,192 number of mapped bases = 1,425,667,041 bp number of sequenced bases = 1,425,371,832 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,854,967 duplication rate = 22.62% >>>>>>> Insert size mean insert size = 128,280.0447 std insert size = 2,778,152.4093 median insert size = 162 >>>>>>> Mapping quality mean mapping quality = 50.6678 >>>>>>> ACTG content number of A's = 417,787,167 bp (29.31%) number of C's = 293,327,504 bp (20.58%) number of T's = 414,862,626 bp (29.11%) number of G's = 299,087,742 bp (20.98%) number of N's = 306,793 bp (0.02%) GC percentage = 41.56% >>>>>>> Mismatches and indels general error rate = 0.0046 number of mismatches = 5,791,111 number of insertions = 235,179 mapped reads with insertion percentage = 1.29% number of deletions = 163,416 mapped reads with deletion percentage = 0.9% homopolymer indels = 35.33% >>>>>>> Coverage mean coverageData = 0.4605X std coverageData = 130.5232X There is a 3.07% of reference with a coverageData >= 1X There is a 1.79% of reference with a coverageData >= 2X There is a 1.25% of reference with a coverageData >= 3X There is a 0.99% of reference with a coverageData >= 4X There is a 0.82% of reference with a coverageData >= 5X There is a 0.7% of reference with a coverageData >= 6X There is a 0.61% of reference with a coverageData >= 7X There is a 0.54% of reference with a coverageData >= 8X There is a 0.49% of reference with a coverageData >= 9X There is a 0.44% of reference with a coverageData >= 10X There is a 0.4% of reference with a coverageData >= 11X There is a 0.37% of reference with a coverageData >= 12X There is a 0.34% of reference with a coverageData >= 13X There is a 0.32% of reference with a coverageData >= 14X There is a 0.3% of reference with a coverageData >= 15X There is a 0.28% of reference with a coverageData >= 16X There is a 0.26% of reference with a coverageData >= 17X There is a 0.25% of reference with a coverageData >= 18X There is a 0.23% of reference with a coverageData >= 19X There is a 0.22% of reference with a coverageData >= 20X There is a 0.21% of reference with a coverageData >= 21X There is a 0.2% of reference with a coverageData >= 22X There is a 0.19% of reference with a coverageData >= 23X There is a 0.18% of reference with a coverageData >= 24X There is a 0.17% of reference with a coverageData >= 25X There is a 0.16% of reference with a coverageData >= 26X There is a 0.16% of reference with a coverageData >= 27X There is a 0.15% of reference with a coverageData >= 28X There is a 0.15% of reference with a coverageData >= 29X There is a 0.14% of reference with a coverageData >= 30X There is a 0.13% of reference with a coverageData >= 31X There is a 0.13% of reference with a coverageData >= 32X There is a 0.13% of reference with a coverageData >= 33X There is a 0.12% of reference with a coverageData >= 34X There is a 0.12% of reference with a coverageData >= 35X There is a 0.11% of reference with a coverageData >= 36X There is a 0.11% of reference with a coverageData >= 37X There is a 0.11% of reference with a coverageData >= 38X There is a 0.1% of reference with a coverageData >= 39X There is a 0.1% of reference with a coverageData >= 40X There is a 0.1% of reference with a coverageData >= 41X There is a 0.1% of reference with a coverageData >= 42X There is a 0.09% of reference with a coverageData >= 43X There is a 0.09% of reference with a coverageData >= 44X There is a 0.09% of reference with a coverageData >= 45X There is a 0.09% of reference with a coverageData >= 46X There is a 0.08% of reference with a coverageData >= 47X There is a 0.08% of reference with a coverageData >= 48X There is a 0.08% of reference with a coverageData >= 49X There is a 0.08% of reference with a coverageData >= 50X There is a 0.08% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 129343953 0.518931316925385 44.89961365415151 chr2 243199373 68988690 0.2836713316690993 37.48656435443234 chr3 198022430 62042009 0.31330798738304544 10.600614776824008 chr4 191154276 48113293 0.25169875352409066 9.527676086465936 chr5 180915260 144310530 0.7976691960645 45.98568895548725 chr6 171115067 258141819 1.5085861433815178 528.5072165732435 chr7 159138663 205420583 1.2908276287328115 107.20795554005282 chr8 146364022 69557215 0.47523437829550763 70.71545667168667 chr9 141213431 76266967 0.5400829542906581 58.00964067075403 chr10 135534747 27930603 0.20607706597925032 9.106392261711209 chr11 135006516 35284274 0.26135237798448185 15.56942488286102 chr12 133851895 30560127 0.22831299474691785 7.625908341624034 chr13 115169878 32118139 0.27887620928104134 7.123771709941289 chr14 107349540 27624098 0.2573285176629541 6.560438114175907 chr15 102531392 13992357 0.13646900453667887 21.05344877998229 chr16 90354753 36245094 0.4011420849105747 55.212612591163406 chr17 81195210 42555585 0.5241144767037366 38.773797668736194 chr18 78077248 24038554 0.3078816763623636 7.335570111460103 chr19 59128983 11542849 0.1952147392759994 16.77270692130827 chr20 63025520 11872137 0.18837031412037536 3.3535669498217193 chr21 48129895 14322661 0.29758346657519197 4.9876585201879085 chr22 51304566 24004160 0.4678757052539924 45.63797905335232 chrMT 16571 223391 13.480840021724699 7.384040464543357 chrX 155270560 24301171 0.1565085551311208 3.3262672883481725 chrY 59373566 6866782 0.1156538584864517 8.075295929207721