BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237306.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,974,756 number of mapped reads = 1,494,117 (75.66%) number of supplementary alignments = 11,567 (0.59%) number of secondary alignments = 0 number of mapped bases = 89,291,240 bp number of sequenced bases = 89,236,883 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 633,340 duplication rate = 23.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.3354 >>>>>>> ACTG content number of A's = 21,977,729 bp (24.63%) number of C's = 15,351,633 bp (17.2%) number of T's = 30,235,375 bp (33.88%) number of G's = 21,663,872 bp (24.28%) number of N's = 8,274 bp (0.01%) GC percentage = 41.48% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 661,784 number of insertions = 6,662 mapped reads with insertion percentage = 0.44% number of deletions = 31,274 mapped reads with deletion percentage = 2.07% homopolymer indels = 44.2% >>>>>>> Coverage mean coverageData = 0.0288X std coverageData = 0.6358X There is a 0.84% of reference with a coverageData >= 1X There is a 0.44% of reference with a coverageData >= 2X There is a 0.33% of reference with a coverageData >= 3X There is a 0.25% of reference with a coverageData >= 4X There is a 0.19% of reference with a coverageData >= 5X There is a 0.15% of reference with a coverageData >= 6X There is a 0.12% of reference with a coverageData >= 7X There is a 0.09% of reference with a coverageData >= 8X There is a 0.08% 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 0.03% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% 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 9089772 0.036468402620348936 0.5935976097919373 chr2 243199373 8585261 0.035301328675711674 1.2141056995049735 chr3 198022430 4761257 0.024044028749672448 0.4123427792665327 chr4 191154276 4229620 0.02212673495203424 0.4365709347346172 chr5 180915260 4962689 0.027431013834874958 0.4523807680893044 chr6 171115067 8536659 0.049888412222636125 0.7516980173672116 chr7 159138663 5379641 0.03380473920407387 0.6147804945907817 chr8 146364022 4522216 0.030897046543309666 0.5437016752256004 chr9 141213431 3971719 0.028125646207123173 0.4842506880572496 chr10 135534747 4290624 0.03165700379401601 0.5738517389758891 chr11 135006516 2881709 0.0213449623424102 0.4412705773819676 chr12 133851895 3548463 0.026510368045218936 0.47677247742580287 chr13 115169878 3591199 0.031181755701781676 0.5492056011464723 chr14 107349540 2335081 0.021752128607164967 0.42215350914896077 chr15 102531392 1875416 0.018291139556556493 0.37068624067789746 chr16 90354753 1974578 0.021853615160676715 0.40073196953300705 chr17 81195210 2131943 0.026257004569604538 0.4533325360212032 chr18 78077248 2310605 0.02959383250803102 1.4938972677662368 chr19 59128983 1225282 0.020722189657819752 0.4188086558868304 chr20 63025520 1505218 0.02388267482759365 0.4441913860654967 chr21 48129895 1314880 0.027319403044614995 0.47907911243478696 chr22 51304566 1086024 0.02116817438822112 0.4232310753427749 chrMT 16571 17699 1.0680707259670508 2.645869315123859 chrX 155270560 4868145 0.0313526595125309 0.529429327086933 chrY 59373566 295540 0.0049776360072426844 0.22616095121733584