BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1505920.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 10,757,471 number of mapped reads = 5,755,739 (53.5%) number of supplementary alignments = 276 (0%) number of secondary alignments = 0 number of mapped bases = 269,346,814 bp number of sequenced bases = 269,288,847 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 292,738 duplication rate = 3.72% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3809 >>>>>>> ACTG content number of A's = 79,575,109 bp (29.55%) number of C's = 54,898,197 bp (20.39%) number of T's = 79,090,745 bp (29.37%) number of G's = 55,723,848 bp (20.69%) number of N's = 948 bp (0%) GC percentage = 41.08% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 1,399,486 number of insertions = 12,183 mapped reads with insertion percentage = 0.21% number of deletions = 41,463 mapped reads with deletion percentage = 0.72% homopolymer indels = 46.11% >>>>>>> Coverage mean coverageData = 0.087X std coverageData = 0.7693X There is a 6.86% of reference with a coverageData >= 1X There is a 1.26% of reference with a coverageData >= 2X There is a 0.29% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% 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 28597493 0.11473388866702161 1.7446381467278254 chr2 243199373 16398679 0.06742895262316322 0.5234997430238666 chr3 198022430 18532227 0.09358650431670797 0.3758386741967844 chr4 191154276 10005822 0.052344222736613016 0.28567497912635387 chr5 180915260 16190168 0.08949033928923408 0.3682244407027171 chr6 171115067 20062018 0.1172428492226228 0.5565651074972549 chr7 159138663 18686090 0.11742017714450699 1.290241758604081 chr8 146364022 16304359 0.11139594811080007 0.9618379712155711 chr9 141213431 7435070 0.052651294904094495 0.4401646625053628 chr10 135534747 9299785 0.06861550418506333 0.8020951665497251 chr11 135006516 14810736 0.10970386051588799 0.672372480813214 chr12 133851895 8065699 0.060258384836464216 0.3239037088458337 chr13 115169878 8166571 0.07090891422147726 0.31819712289410496 chr14 107349540 10556829 0.09834070085442378 0.5652398986640398 chr15 102531392 5076961 0.04951616184046346 0.2642488838570897 chr16 90354753 9426437 0.1043269632976585 0.5044970102767425 chr17 81195210 4730092 0.058255801050332894 0.34895202170043815 chr18 78077248 6551481 0.0839102448897789 0.9211487125415033 chr19 59128983 7026226 0.1188287983914758 1.1415180265399323 chr20 63025520 7311919 0.11601521098120253 0.4276125148883774 chr21 48129895 4080411 0.0847791377895173 0.380439778456038 chr22 51304566 1918033 0.03738523000077615 0.23223798001456017 chrMT 16571 6496 0.39201013819322916 0.7401313861664386 chrX 155270560 19276862 0.12415014153359143 0.5120998887868575 chrY 59373566 830350 0.013985179869438868 0.19494468150208977