BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617360.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 = 30,586,377 (95.58%) number of supplementary alignments = 67,570 (0.21%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,376,429 number of mapped paired reads (second in pair) = 15,209,948 number of mapped paired reads (both in pair) = 30,075,602 number of mapped paired reads (singletons) = 510,775 number of mapped bases = 3,009,275,356 bp number of sequenced bases = 3,008,378,847 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,583,917 duplication rate = 1.48% >>>>>>> Insert size mean insert size = 56,773.6698 std insert size = 2,268,129.8354 median insert size = 215 >>>>>>> Mapping quality mean mapping quality = 53.5066 >>>>>>> ACTG content number of A's = 908,272,072 bp (30.19%) number of C's = 599,189,081 bp (19.92%) number of T's = 897,343,420 bp (29.83%) number of G's = 602,279,237 bp (20.02%) number of N's = 1,295,037 bp (0.04%) GC percentage = 39.94% >>>>>>> Mismatches and indels general error rate = 0.0103 number of mismatches = 30,164,808 number of insertions = 303,232 mapped reads with insertion percentage = 0.96% number of deletions = 370,554 mapped reads with deletion percentage = 1.17% homopolymer indels = 41.27% >>>>>>> Coverage mean coverageData = 0.9721X std coverageData = 9.8662X There is a 53.65% of reference with a coverageData >= 1X There is a 24.41% of reference with a coverageData >= 2X There is a 9.43% of reference with a coverageData >= 3X There is a 3.32% of reference with a coverageData >= 4X There is a 1.14% of reference with a coverageData >= 5X There is a 0.42% of reference with a coverageData >= 6X There is a 0.18% of reference with a coverageData >= 7X There is a 0.1% 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 0.02% 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 0.01% 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 195697808 0.78514471584807 20.1009463511405 chr2 243199373 296805441 1.220420255770972 8.900781693449565 chr3 198022430 239318294 1.2085413455435325 1.4763048143574702 chr4 191154276 164328783 0.8596657445423821 9.701060135062349 chr5 180915260 188121634 1.039832869819826 1.4734897818723918 chr6 171115067 140864446 0.8232147435620032 3.7071584133174547 chr7 159138663 243954499 1.5329681323262092 10.852070160565903 chr8 146364022 126332530 0.8631392351325246 7.771331149714361 chr9 141213431 126978848 0.8991980939830008 15.150805106032662 chr10 135534747 126524031 0.933517299442039 19.960806819154094 chr11 135006516 161733574 1.197968652120465 5.550897279140983 chr12 133851895 132589791 0.9905708918054541 1.349948295639882 chr13 115169878 130613441 1.1340937688585553 1.2976412533674504 chr14 107349540 86942013 0.8098964653225342 1.3944445909942151 chr15 102531392 67817746 0.6614339733142411 0.9825642746726687 chr16 90354753 75864094 0.8396248285909209 7.8795991975247315 chr17 81195210 94577887 1.1648210159195351 7.1245872979724 chr18 78077248 54668175 0.7001806083124241 15.602168572605636 chr19 59128983 56425925 0.9542853967232956 9.661070904687906 chr20 63025520 86968702 1.3798966196550222 2.4380633656592368 chr21 48129895 47870934 0.994619539477491 3.25305679800845 chr22 51304566 27124800 0.5287014804881109 0.9276530317418512 chrMT 16571 2085922 125.87785891014423 20.988913627842745 chrX 155270560 124754609 0.8034659564569098 3.0314122609092764 chrY 59373566 10311429 0.17367036704515945 8.438997031518271