BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124917.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 6,536,394 number of mapped reads = 6,464,681 (98.9%) number of supplementary alignments = 29,762 (0.46%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,234,866 number of mapped paired reads (second in pair) = 3,229,815 number of mapped paired reads (both in pair) = 6,440,912 number of mapped paired reads (singletons) = 23,769 number of mapped bases = 585,730,603 bp number of sequenced bases = 585,395,796 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 405,458 duplication rate = 3.59% >>>>>>> Insert size mean insert size = 81,909.5579 std insert size = 2,723,402.5392 median insert size = 170 >>>>>>> Mapping quality mean mapping quality = 52.744 >>>>>>> ACTG content number of A's = 169,145,527 bp (28.89%) number of C's = 116,389,905 bp (19.88%) number of T's = 170,156,898 bp (29.07%) number of G's = 129,693,841 bp (22.15%) number of N's = 9,625 bp (0%) GC percentage = 42.04% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 4,284,208 number of insertions = 96,130 mapped reads with insertion percentage = 1.44% number of deletions = 191,736 mapped reads with deletion percentage = 2.9% homopolymer indels = 45.46% >>>>>>> Coverage mean coverageData = 0.1892X std coverageData = 1.8519X There is a 11.84% of reference with a coverageData >= 1X There is a 4.14% of reference with a coverageData >= 2X There is a 1.32% of reference with a coverageData >= 3X There is a 0.49% of reference with a coverageData >= 4X There is a 0.19% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% 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 0.01% 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 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% 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 44056576 0.17675613333777812 2.55894959210962 chr2 243199373 55804966 0.22946180046278328 2.3058270839300925 chr3 198022430 37985126 0.19182234052980765 0.6300710677383831 chr4 191154276 25542944 0.13362475867398332 1.5801680479919877 chr5 180915260 37944365 0.2097355690172294 0.6588507653365517 chr6 171115067 23240335 0.13581699968010416 1.4017754529866961 chr7 159138663 38812630 0.2438918944543351 2.517286582697367 chr8 146364022 37102630 0.2534955619079667 0.9271146955460832 chr9 141213431 28037502 0.19854699231831566 2.1485105523515475 chr10 135534747 24411780 0.18011455025625273 4.49554523569228 chr11 135006516 30003756 0.2222393176933771 1.198098608556879 chr12 133851895 36054852 0.2693637770313226 0.732818266828219 chr13 115169878 23267139 0.20202451720926543 0.6313998533889795 chr14 107349540 19288331 0.17967781697061766 0.6756900643006347 chr15 102531392 15300081 0.14922338126453993 0.5271822396720885 chr16 90354753 18870523 0.20884925666279006 2.7500118863932577 chr17 81195210 10169898 0.1252524379209069 1.0802503667377024 chr18 78077248 14594684 0.1869262092844256 2.2684944417801214 chr19 59128983 7753695 0.13113188501821518 1.4599646507551713 chr20 63025520 11085068 0.1758822140618594 0.7067903204435196 chr21 48129895 6396743 0.13290581664472778 0.8187354421419606 chr22 51304566 5702288 0.1111458188731194 0.5121537561493661 chrMT 16571 155062 9.357431657715285 6.7083946540670265 chrX 155270560 32323589 0.20817590275967318 1.0491899369505562 chrY 59373566 1826040 0.030755100678978926 2.024858583863314