BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695927.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.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 = 8,780,044 number of mapped reads = 7,880,889 (89.76%) number of supplementary alignments = 170,536 (1.94%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,970,299 number of mapped paired reads (second in pair) = 3,910,590 number of mapped paired reads (both in pair) = 7,411,914 number of mapped paired reads (singletons) = 468,975 number of mapped bases = 655,966,180 bp number of sequenced bases = 655,726,204 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,003,093 duplication rate = 15.51% >>>>>>> Insert size mean insert size = 168,511.0146 std insert size = 3,936,261.2208 median insert size = 294 >>>>>>> Mapping quality mean mapping quality = 51.6374 >>>>>>> ACTG content number of A's = 173,410,029 bp (26.45%) number of C's = 116,160,844 bp (17.71%) number of T's = 214,430,192 bp (32.7%) number of G's = 151,521,560 bp (23.11%) number of N's = 203,579 bp (0.03%) GC percentage = 40.82% >>>>>>> Mismatches and indels general error rate = 0.0139 number of mismatches = 9,025,362 number of insertions = 53,088 mapped reads with insertion percentage = 0.66% number of deletions = 135,369 mapped reads with deletion percentage = 1.69% homopolymer indels = 45% >>>>>>> Coverage mean coverageData = 0.2119X std coverageData = 1.7805X There is a 11% of reference with a coverageData >= 1X There is a 4.22% of reference with a coverageData >= 2X There is a 1.99% of reference with a coverageData >= 3X There is a 1.09% of reference with a coverageData >= 4X There is a 0.67% of reference with a coverageData >= 5X There is a 0.45% of reference with a coverageData >= 6X There is a 0.32% of reference with a coverageData >= 7X There is a 0.23% of reference with a coverageData >= 8X There is a 0.17% of reference with a coverageData >= 9X There is a 0.13% of reference with a coverageData >= 10X There is a 0.1% of reference with a coverageData >= 11X There is a 0.08% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.04% 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 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% 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 0.01% of reference with a coverageData >= 25X There is a 0.01% 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% 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 54551695 0.21886282481920075 2.969584348647489 chr2 243199373 57602738 0.23685397412599415 2.2064784686581294 chr3 198022430 46514163 0.2348934057621654 0.9065099648625624 chr4 191154276 45534563 0.2382084458314707 1.0133269349123974 chr5 180915260 42717683 0.23611984417455995 0.9642870248963035 chr6 171115067 40122072 0.2344742207885177 1.290549667789286 chr7 159138663 36334287 0.22831841310618525 2.3775805253529274 chr8 146364022 35365658 0.24162808261718854 2.7821224129008506 chr9 141213431 27656660 0.1958500675477533 1.7200566211322292 chr10 135534747 31900803 0.23536992325665387 2.0751717515489565 chr11 135006516 30779627 0.227986232901529 1.9953284379593021 chr12 133851895 30245976 0.22596599024615976 0.9266135905781807 chr13 115169878 22760222 0.1976230451507468 0.8302317410336286 chr14 107349540 20506955 0.19102974265190145 0.9448994990393368 chr15 102531392 18206009 0.1775652182699324 0.7960581755712404 chr16 90354753 16802633 0.1859629122111595 0.9183520295331736 chr17 81195210 15092702 0.18588167947345663 1.0208342368433367 chr18 78077248 18595721 0.23817080489312328 2.962113592544338 chr19 59128983 9598768 0.16233609159149584 2.3096254242058296 chr20 63025520 12600581 0.19992823541955704 0.8712795978934144 chr21 48129895 9131092 0.1897176796251062 1.6722924536792592 chr22 51304566 6230234 0.12143624799398946 1.2686503177298427 chrMT 16571 851369 51.3770442339026 40.040561339946876 chrX 155270560 20071216 0.12926607593867118 0.8805517612506136 chrY 59373566 6192753 0.10430151694105758 1.104152675778296