BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173983.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 3,908,282 number of mapped reads = 3,824,216 (97.85%) number of supplementary alignments = 518,308 (13.26%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,912,008 number of mapped paired reads (second in pair) = 1,912,208 number of mapped paired reads (both in pair) = 3,769,222 number of mapped paired reads (singletons) = 54,994 number of mapped bases = 435,922,442 bp number of sequenced bases = 435,608,700 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,059,009 duplication rate = 64.59% >>>>>>> Insert size mean insert size = 1,218,754.1904 std insert size = 10,472,267.3666 median insert size = 159 >>>>>>> Mapping quality mean mapping quality = 52.5271 >>>>>>> ACTG content number of A's = 129,437,460 bp (29.71%) number of C's = 86,971,782 bp (19.97%) number of T's = 128,683,422 bp (29.54%) number of G's = 90,512,407 bp (20.78%) number of N's = 3,629 bp (0%) GC percentage = 40.74% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 3,692,277 number of insertions = 48,009 mapped reads with insertion percentage = 1.21% number of deletions = 134,886 mapped reads with deletion percentage = 3.44% homopolymer indels = 40.68% >>>>>>> Coverage mean coverageData = 0.1408X std coverageData = 2.4962X There is a 3.1% of reference with a coverageData >= 1X There is a 2.31% of reference with a coverageData >= 2X There is a 1.72% of reference with a coverageData >= 3X There is a 1.37% of reference with a coverageData >= 4X There is a 1.02% of reference with a coverageData >= 5X There is a 0.84% of reference with a coverageData >= 6X There is a 0.62% of reference with a coverageData >= 7X There is a 0.53% of reference with a coverageData >= 8X There is a 0.4% of reference with a coverageData >= 9X There is a 0.36% of reference with a coverageData >= 10X There is a 0.26% of reference with a coverageData >= 11X There is a 0.24% of reference with a coverageData >= 12X There is a 0.18% of reference with a coverageData >= 13X There is a 0.16% of reference with a coverageData >= 14X There is a 0.12% of reference with a coverageData >= 15X There is a 0.11% of reference with a coverageData >= 16X There is a 0.08% of reference with a coverageData >= 17X There is a 0.08% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.05% 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 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% 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 33764535 0.13546419609522256 1.404637355532507 chr2 243199373 42452722 0.1745593398384296 7.717319060123148 chr3 198022430 29108247 0.14699469650988528 1.1394801105386339 chr4 191154276 26241520 0.13727927279011012 1.3962035746574448 chr5 180915260 26198221 0.14480934886310862 1.1329658836193714 chr6 171115067 26035503 0.15215201943613768 1.2434788229843754 chr7 159138663 24370873 0.15314237621815385 1.5529945023179916 chr8 146364022 23135204 0.1580661947100634 1.6539452472784537 chr9 141213431 19182122 0.13583780143405763 1.3326158531794696 chr10 135534747 21294007 0.15711105433354297 1.7258263776233087 chr11 135006516 18014066 0.13343108565219178 1.0911829302833957 chr12 133851895 19637954 0.14671405287164593 1.1648152183108007 chr13 115169878 15100197 0.131112381659378 1.0792060661944025 chr14 107349540 13507163 0.12582413487752253 1.0499869696342596 chr15 102531392 12493140 0.12184697541217425 1.0399626910765585 chr16 90354753 13830425 0.15306804059328236 1.3339837536528532 chr17 81195210 11729703 0.1444629923366169 1.1465566492777197 chr18 78077248 12340424 0.15805403387168565 1.711349351137658 chr19 59128983 8859518 0.14983376257291622 1.336453210424976 chr20 63025520 9931657 0.15758151618582442 1.2327803387250744 chr21 48129895 6494137 0.1349293822477693 1.3429486734355924 chr22 51304566 5848967 0.1140048041727904 1.128842489025885 chrMT 16571 481568 29.06088950576308 26.0206239202977 chrX 155270560 12401253 0.07986866924418898 0.8405483293473528 chrY 59373566 3469316 0.05843199648813413 0.9695872453234088