BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085142.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,348,751 number of mapped reads = 2,111,417 (89.9%) number of supplementary alignments = 18,364 (0.78%) number of secondary alignments = 0 number of mapped bases = 141,453,612 bp number of sequenced bases = 141,401,875 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 76,538 duplication rate = 2.81% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4137 >>>>>>> ACTG content number of A's = 39,363,229 bp (27.84%) number of C's = 26,417,535 bp (18.68%) number of T's = 44,042,460 bp (31.15%) number of G's = 31,548,643 bp (22.31%) number of N's = 30,008 bp (0.02%) GC percentage = 40.99% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,242,877 number of insertions = 11,144 mapped reads with insertion percentage = 0.52% number of deletions = 31,900 mapped reads with deletion percentage = 1.5% homopolymer indels = 47.05% >>>>>>> Coverage mean coverageData = 0.0457X std coverageData = 0.3722X There is a 4.02% of reference with a coverageData >= 1X There is a 0.41% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% 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 11314396 0.045393652198764234 0.6266386313870805 chr2 243199373 11833343 0.048656963437154914 0.45633230150690934 chr3 198022430 9619737 0.0485790271334414 0.24273600440598878 chr4 191154276 9506451 0.04973182498936095 0.2541481695275138 chr5 180915260 8805472 0.04867180358362252 0.24460725505387304 chr6 171115067 8381880 0.04898388053694886 0.289783427237807 chr7 159138663 7681753 0.04827081524494145 0.477493335048661 chr8 146364022 7276401 0.04971441000712593 0.5865831080876553 chr9 141213431 5898645 0.04177113294556238 0.34381022939915434 chr10 135534747 6573886 0.04850332586668716 0.32852011551885585 chr11 135006516 6405693 0.04744728765536028 0.31239527662988825 chr12 133851895 6448600 0.04817712890803675 0.24474956565453915 chr13 115169878 4594103 0.03988979653169382 0.22350850605175465 chr14 107349540 4303544 0.040089077233120884 0.23250417803045884 chr15 102531392 4121988 0.04020220460871145 0.22749498078468527 chr16 90354753 3903927 0.04320665897896926 0.25426399732844723 chr17 81195210 3687325 0.04541308532855571 0.25471145556514546 chr18 78077248 3794564 0.04860012484046569 0.6093523818735972 chr19 59128983 2692843 0.04554184535864586 0.48573149136975263 chr20 63025520 2728424 0.04329078125813163 0.23526284776808673 chr21 48129895 1883319 0.03912992122671367 0.23007854777445472 chr22 51304566 1427707 0.027828068948093237 0.1826635964456394 chrMT 16571 5943 0.35863858548065897 0.6771176976495635 chrX 155270560 8219420 0.05293611358135116 0.280714835062855 chrY 59373566 344248 0.005798001083512484 0.11939707429819942