BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124806.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 = 856,652 number of mapped reads = 854,933 (99.8%) number of supplementary alignments = 405,071 (47.29%) number of secondary alignments = 0 number of mapped bases = 127,489,776 bp number of sequenced bases = 127,456,505 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,252,573 duplication rate = 6.67% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2532 >>>>>>> ACTG content number of A's = 36,268,910 bp (28.46%) number of C's = 22,352,115 bp (17.54%) number of T's = 42,708,052 bp (33.51%) number of G's = 26,127,428 bp (20.5%) number of N's = 0 bp (0%) GC percentage = 38.04% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 1,015,817 number of insertions = 12,441 mapped reads with insertion percentage = 1.45% number of deletions = 32,257 mapped reads with deletion percentage = 3.72% homopolymer indels = 54.03% >>>>>>> Coverage mean coverageData = 0.0412X std coverageData = 116.0534X There is a 0.03% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 1892465 0.007592618996925187 6.810975670595504 chr2 243199373 113809 4.679658446323379E-4 0.1279961672564255 chr3 198022430 61931 3.1274739937288924E-4 0.03573181600951327 chr4 191154276 221526 0.0011588859252094365 0.9883874162953795 chr5 180915260 46657 2.5789422075285414E-4 0.016157906692465914 chr6 171115067 46077 2.6927494350921185E-4 0.041864647482195254 chr7 159138663 45973 2.888864285607326E-4 0.03208067934608276 chr8 146364022 1361273 0.009300598476311343 6.053622313367216 chr9 141213431 34193 2.4213702448742288E-4 0.015862669486089616 chr10 135534747 123266572 0.9094831748201072 554.5257705577857 chr11 135006516 37571 2.7829027155992976E-4 0.02449030699518174 chr12 133851895 36439 2.722337251930576E-4 0.016957296508772007 chr13 115169878 22523 1.9556328782426946E-4 0.01407493726801227 chr14 107349540 26050 2.4266522241269035E-4 0.05994550683878858 chr15 102531392 38845 3.788595789277883E-4 0.07408439612836973 chr16 90354753 32284 3.573027309365784E-4 0.04505888152908725 chr17 81195210 21632 2.6641965702163957E-4 0.01790808465280857 chr18 78077248 39180 5.018107195581484E-4 0.08286310479326633 chr19 59128983 60748 0.0010273811068253955 0.33900421027821437 chr20 63025520 19434 3.0835128373395414E-4 0.018873816509109416 chr21 48129895 10418 2.1645590542011364E-4 0.014793946089088015 chr22 51304566 7935 1.5466459651953786E-4 0.012632953488582697 chrMT 16571 654 0.03946653792770503 0.194702157953388 chrX 155270560 30474 1.9626386354245132E-4 0.014773773017799958 chrY 59373566 15113 2.5454088440637034E-4 0.024142737423417646