BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472537.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 = 18,075,938 number of mapped reads = 17,742,293 (98.15%) number of supplementary alignments = 61,199 (0.34%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,922,360 number of mapped paired reads (second in pair) = 8,819,933 number of mapped paired reads (both in pair) = 17,573,700 number of mapped paired reads (singletons) = 168,593 number of mapped bases = 1,745,242,732 bp number of sequenced bases = 1,745,002,058 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,218,407 duplication rate = 46.53% >>>>>>> Insert size mean insert size = 27,558.5749 std insert size = 1,626,439.5984 median insert size = 241 >>>>>>> Mapping quality mean mapping quality = 54.8908 >>>>>>> ACTG content number of A's = 487,276,404 bp (27.92%) number of C's = 387,749,078 bp (22.22%) number of T's = 483,647,020 bp (27.72%) number of G's = 386,059,807 bp (22.12%) number of N's = 269,749 bp (0.02%) GC percentage = 44.34% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 10,873,154 number of insertions = 99,362 mapped reads with insertion percentage = 0.55% number of deletions = 100,935 mapped reads with deletion percentage = 0.56% homopolymer indels = 45.09% >>>>>>> Coverage mean coverageData = 0.5638X std coverageData = 19.3133X There is a 5.54% of reference with a coverageData >= 1X There is a 2.46% of reference with a coverageData >= 2X There is a 1.08% of reference with a coverageData >= 3X There is a 0.75% of reference with a coverageData >= 4X There is a 0.54% of reference with a coverageData >= 5X There is a 0.47% of reference with a coverageData >= 6X There is a 0.41% of reference with a coverageData >= 7X There is a 0.39% of reference with a coverageData >= 8X There is a 0.37% of reference with a coverageData >= 9X There is a 0.35% of reference with a coverageData >= 10X There is a 0.34% of reference with a coverageData >= 11X There is a 0.32% of reference with a coverageData >= 12X There is a 0.31% of reference with a coverageData >= 13X There is a 0.31% of reference with a coverageData >= 14X There is a 0.3% of reference with a coverageData >= 15X There is a 0.29% of reference with a coverageData >= 16X There is a 0.28% of reference with a coverageData >= 17X There is a 0.27% of reference with a coverageData >= 18X There is a 0.27% of reference with a coverageData >= 19X There is a 0.26% of reference with a coverageData >= 20X There is a 0.26% of reference with a coverageData >= 21X There is a 0.25% of reference with a coverageData >= 22X There is a 0.25% of reference with a coverageData >= 23X There is a 0.24% of reference with a coverageData >= 24X There is a 0.24% of reference with a coverageData >= 25X There is a 0.23% of reference with a coverageData >= 26X There is a 0.23% of reference with a coverageData >= 27X There is a 0.22% of reference with a coverageData >= 28X There is a 0.22% of reference with a coverageData >= 29X There is a 0.22% of reference with a coverageData >= 30X There is a 0.21% of reference with a coverageData >= 31X There is a 0.21% of reference with a coverageData >= 32X There is a 0.21% of reference with a coverageData >= 33X There is a 0.2% of reference with a coverageData >= 34X There is a 0.2% of reference with a coverageData >= 35X There is a 0.2% of reference with a coverageData >= 36X There is a 0.19% of reference with a coverageData >= 37X There is a 0.19% of reference with a coverageData >= 38X There is a 0.19% of reference with a coverageData >= 39X There is a 0.19% of reference with a coverageData >= 40X There is a 0.18% of reference with a coverageData >= 41X There is a 0.18% of reference with a coverageData >= 42X There is a 0.18% of reference with a coverageData >= 43X There is a 0.18% of reference with a coverageData >= 44X There is a 0.17% of reference with a coverageData >= 45X There is a 0.17% of reference with a coverageData >= 46X There is a 0.17% of reference with a coverageData >= 47X There is a 0.17% of reference with a coverageData >= 48X There is a 0.17% of reference with a coverageData >= 49X There is a 0.16% of reference with a coverageData >= 50X There is a 0.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 162361199 0.65139737003905 19.533835065354964 chr2 243199373 100835887 0.41462231483631334 15.24470451741368 chr3 198022430 212613147 1.0736821429774395 25.40601609353843 chr4 191154276 74277084 0.3885713966450847 14.059715170879109 chr5 180915260 96070295 0.5310237234824746 18.66353374443979 chr6 171115067 138724015 0.8107060204113995 25.09200156786371 chr7 159138663 64191714 0.40336969527009287 11.673177325874587 chr8 146364022 81401281 0.5561563551458022 16.650279494009748 chr9 141213431 83303175 0.5899097161657378 13.92946760329279 chr10 135534747 40123778 0.2960405275261258 13.67171490685414 chr11 135006516 68834239 0.5098586426746987 17.92368087452547 chr12 133851895 101370065 0.7573300699254202 22.395024592982093 chr13 115169878 55238888 0.4796296476062951 25.106408014650956 chr14 107349540 55582858 0.5177745335471395 19.94881394762152 chr15 102531392 36797512 0.3588902021343863 10.90517896289492 chr16 90354753 53034070 0.5869538484599698 19.847900272428465 chr17 81195210 57337787 0.7061720389663381 17.248327112801014 chr18 78077248 30426603 0.3896987122292015 17.51929892644563 chr19 59128983 55749502 0.9428456092336308 32.749080195684144 chr20 63025520 38555834 0.6117495579568404 20.5828596420651 chr21 48129895 8677751 0.18029856495635405 6.888098752143998 chr22 51304566 14417164 0.28101132363150677 8.123755293436108 chrMT 16571 4978 0.30040432080140006 0.847868868369438 chrX 155270560 111182259 0.7160549881445653 29.331137359550887 chrY 59373566 4131647 0.06958731432772625 2.861696892129979