BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617386.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 30,287,829 (94.65%) number of supplementary alignments = 94,813 (0.3%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,232,158 number of mapped paired reads (second in pair) = 15,055,671 number of mapped paired reads (both in pair) = 29,724,184 number of mapped paired reads (singletons) = 563,645 number of mapped bases = 2,967,137,123 bp number of sequenced bases = 2,966,256,325 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,614,376 duplication rate = 1.52% >>>>>>> Insert size mean insert size = 64,306.9792 std insert size = 2,419,057.3581 median insert size = 211 >>>>>>> Mapping quality mean mapping quality = 53.4081 >>>>>>> ACTG content number of A's = 899,586,120 bp (30.33%) number of C's = 588,047,009 bp (19.82%) number of T's = 887,897,836 bp (29.93%) number of G's = 589,931,706 bp (19.89%) number of N's = 793,654 bp (0.03%) GC percentage = 39.71% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 29,220,417 number of insertions = 301,066 mapped reads with insertion percentage = 0.96% number of deletions = 365,100 mapped reads with deletion percentage = 1.17% homopolymer indels = 41.27% >>>>>>> Coverage mean coverageData = 0.9585X std coverageData = 9.883X There is a 53.01% of reference with a coverageData >= 1X There is a 23.97% of reference with a coverageData >= 2X There is a 9.23% of reference with a coverageData >= 3X There is a 3.25% of reference with a coverageData >= 4X There is a 1.12% of reference with a coverageData >= 5X There is a 0.41% of reference with a coverageData >= 6X There is a 0.18% of reference with a coverageData >= 7X There is a 0.11% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% 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 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 192722928 0.7732094196066216 20.102340623729052 chr2 243199373 293015021 1.2048346070365896 8.944957539303658 chr3 198022430 236273888 1.1931672992801876 1.4829191149462837 chr4 191154276 162925148 0.8523228012958497 9.432874366087532 chr5 180915260 186127950 1.0288128817878603 1.4679764706166787 chr6 171115067 139091862 0.8128557259075263 3.6907536818655537 chr7 159138663 240804426 1.5131736151383903 10.865630856574425 chr8 146364022 124977197 0.8538792204002156 7.759205632957036 chr9 141213431 125048738 0.8855300598142113 15.073115707738488 chr10 135534747 125292992 0.9244344699296927 20.387055939671242 chr11 135006516 159270807 1.1797268140746628 5.706416531043648 chr12 133851895 130651779 0.9760921128535386 1.4044178751483916 chr13 115169878 129233796 1.1221145515149369 1.3357913096797458 chr14 107349540 85774454 0.7990202286847247 1.374685515096896 chr15 102531392 66777698 0.6512902702032954 1.1007603414574663 chr16 90354753 74283599 0.822132721673203 7.952736664419142 chr17 81195210 92348658 1.137365837221186 7.130854770961114 chr18 78077248 53646213 0.687091494310865 15.347464427070845 chr19 59128983 54801203 0.9268078059113583 9.635367317554476 chr20 63025520 84793792 1.3453882173443392 2.4568525078562735 chr21 48129895 47103761 0.9786799036233094 3.2082755563599763 chr22 51304566 26285926 0.5123506161225494 0.9273966593103241 chrMT 16571 2011264 121.37251825478245 21.624986720763452 chrX 155270560 123706962 0.7967187211793401 3.0969853226741204 chrY 59373566 10167061 0.171238847267486 8.459453788144982