BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472696.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 11,759,980 number of mapped reads = 11,677,602 (99.3%) number of supplementary alignments = 82,081 (0.7%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,863,679 number of mapped paired reads (second in pair) = 5,813,923 number of mapped paired reads (both in pair) = 11,623,880 number of mapped paired reads (singletons) = 53,722 number of mapped bases = 1,147,715,113 bp number of sequenced bases = 1,147,549,992 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,615,745 duplication rate = 45.1% >>>>>>> Insert size mean insert size = 21,148.6086 std insert size = 1,414,622.7037 median insert size = 207 >>>>>>> Mapping quality mean mapping quality = 54.5465 >>>>>>> ACTG content number of A's = 310,615,987 bp (27.07%) number of C's = 261,939,137 bp (22.83%) number of T's = 316,063,907 bp (27.54%) number of G's = 258,680,632 bp (22.54%) number of N's = 250,329 bp (0.02%) GC percentage = 45.37% >>>>>>> Mismatches and indels general error rate = 0.0042 number of mismatches = 4,636,035 number of insertions = 74,133 mapped reads with insertion percentage = 0.63% number of deletions = 58,762 mapped reads with deletion percentage = 0.49% homopolymer indels = 46.34% >>>>>>> Coverage mean coverageData = 0.3707X std coverageData = 32.5312X There is a 2.25% of reference with a coverageData >= 1X There is a 1.07% of reference with a coverageData >= 2X There is a 0.54% of reference with a coverageData >= 3X There is a 0.41% of reference with a coverageData >= 4X There is a 0.31% of reference with a coverageData >= 5X There is a 0.27% of reference with a coverageData >= 6X There is a 0.24% of reference with a coverageData >= 7X There is a 0.22% of reference with a coverageData >= 8X There is a 0.2% of reference with a coverageData >= 9X There is a 0.19% of reference with a coverageData >= 10X There is a 0.18% of reference with a coverageData >= 11X There is a 0.17% of reference with a coverageData >= 12X There is a 0.17% of reference with a coverageData >= 13X There is a 0.16% of reference with a coverageData >= 14X There is a 0.15% of reference with a coverageData >= 15X There is a 0.15% of reference with a coverageData >= 16X There is a 0.14% of reference with a coverageData >= 17X There is a 0.14% of reference with a coverageData >= 18X There is a 0.14% of reference with a coverageData >= 19X There is a 0.13% of reference with a coverageData >= 20X There is a 0.13% of reference with a coverageData >= 21X There is a 0.13% of reference with a coverageData >= 22X There is a 0.12% of reference with a coverageData >= 23X There is a 0.12% of reference with a coverageData >= 24X There is a 0.12% of reference with a coverageData >= 25X There is a 0.11% of reference with a coverageData >= 26X There is a 0.11% of reference with a coverageData >= 27X There is a 0.11% of reference with a coverageData >= 28X There is a 0.11% of reference with a coverageData >= 29X There is a 0.1% of reference with a coverageData >= 30X There is a 0.1% of reference with a coverageData >= 31X There is a 0.1% of reference with a coverageData >= 32X There is a 0.1% of reference with a coverageData >= 33X There is a 0.1% of reference with a coverageData >= 34X There is a 0.1% of reference with a coverageData >= 35X There is a 0.09% of reference with a coverageData >= 36X There is a 0.09% of reference with a coverageData >= 37X There is a 0.09% of reference with a coverageData >= 38X There is a 0.09% of reference with a coverageData >= 39X There is a 0.09% of reference with a coverageData >= 40X There is a 0.09% of reference with a coverageData >= 41X There is a 0.09% of reference with a coverageData >= 42X There is a 0.08% of reference with a coverageData >= 43X There is a 0.08% of reference with a coverageData >= 44X There is a 0.08% of reference with a coverageData >= 45X There is a 0.08% 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 277791807 1.114507983512707 85.69845491958532 chr2 243199373 56217517 0.2311581494085513 12.315948074356463 chr3 198022430 108854053 0.549705672231171 34.81528970006451 chr4 191154276 31912848 0.16694812518868268 11.437157109240369 chr5 180915260 40114002 0.22172812840663633 12.573190121767318 chr6 171115067 69014358 0.40332133931841313 24.516212074363803 chr7 159138663 50196064 0.3154234367295143 15.58661384670073 chr8 146364022 51626693 0.3527280290234167 23.102123945594414 chr9 141213431 48561170 0.34388492409054205 31.804094144132442 chr10 135534747 33568513 0.2476745907822442 18.334153375742375 chr11 135006516 57493929 0.42586040069354875 35.28398934263211 chr12 133851895 34558125 0.2581818135634165 13.794054274884605 chr13 115169878 36672170 0.3184180676131306 41.85876995419399 chr14 107349540 21177764 0.19727857240934615 14.167493251955264 chr15 102531392 14058655 0.13711561625926233 10.03603323196792 chr16 90354753 45798039 0.5068691737777203 27.609596809955463 chr17 81195210 47632819 0.5866456777437979 25.637217191636005 chr18 78077248 10835999 0.13878561652172985 7.599565995584225 chr19 59128983 24850268 0.42027220390379455 17.622015221531758 chr20 63025520 27768225 0.44058700348684154 29.946723802328705 chr21 48129895 13221349 0.2747013888145819 30.12503074370681 chr22 51304566 23843600 0.4647461592404855 23.503715704542635 chrMT 16571 5562 0.33564661155029873 0.7862037126734495 chrX 155270560 20078055 0.1293101216354214 5.738064888269049 chrY 59373566 1863529 0.03138650961271216 3.7267162735678054