BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695930.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 = 29,872,826 number of mapped reads = 25,736,935 (86.16%) number of supplementary alignments = 800,419 (2.68%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 13,210,146 number of mapped paired reads (second in pair) = 12,526,789 number of mapped paired reads (both in pair) = 24,056,142 number of mapped paired reads (singletons) = 1,680,793 number of mapped bases = 2,127,562,766 bp number of sequenced bases = 2,126,720,601 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,213,363 duplication rate = 21.9% >>>>>>> Insert size mean insert size = 140,062.0431 std insert size = 3,596,720.9553 median insert size = 317 >>>>>>> Mapping quality mean mapping quality = 51.7112 >>>>>>> ACTG content number of A's = 549,018,601 bp (25.82%) number of C's = 376,308,117 bp (17.69%) number of T's = 698,541,508 bp (32.85%) number of G's = 500,626,121 bp (23.54%) number of N's = 2,226,254 bp (0.1%) GC percentage = 41.23% >>>>>>> Mismatches and indels general error rate = 0.0127 number of mismatches = 26,712,158 number of insertions = 170,538 mapped reads with insertion percentage = 0.65% number of deletions = 478,419 mapped reads with deletion percentage = 1.83% homopolymer indels = 46.89% >>>>>>> Coverage mean coverageData = 0.6873X std coverageData = 7.0163X There is a 14.15% of reference with a coverageData >= 1X There is a 7.87% of reference with a coverageData >= 2X There is a 5.69% of reference with a coverageData >= 3X There is a 4.47% of reference with a coverageData >= 4X There is a 3.62% of reference with a coverageData >= 5X There is a 2.99% of reference with a coverageData >= 6X There is a 2.49% of reference with a coverageData >= 7X There is a 2.09% of reference with a coverageData >= 8X There is a 1.77% of reference with a coverageData >= 9X There is a 1.5% of reference with a coverageData >= 10X There is a 1.29% of reference with a coverageData >= 11X There is a 1.11% of reference with a coverageData >= 12X There is a 0.97% of reference with a coverageData >= 13X There is a 0.85% of reference with a coverageData >= 14X There is a 0.76% of reference with a coverageData >= 15X There is a 0.68% of reference with a coverageData >= 16X There is a 0.62% of reference with a coverageData >= 17X There is a 0.57% of reference with a coverageData >= 18X There is a 0.52% of reference with a coverageData >= 19X There is a 0.48% of reference with a coverageData >= 20X There is a 0.45% of reference with a coverageData >= 21X There is a 0.43% of reference with a coverageData >= 22X There is a 0.4% of reference with a coverageData >= 23X There is a 0.38% of reference with a coverageData >= 24X There is a 0.37% of reference with a coverageData >= 25X There is a 0.35% of reference with a coverageData >= 26X There is a 0.34% of reference with a coverageData >= 27X There is a 0.32% of reference with a coverageData >= 28X There is a 0.31% of reference with a coverageData >= 29X There is a 0.3% of reference with a coverageData >= 30X There is a 0.29% of reference with a coverageData >= 31X There is a 0.28% of reference with a coverageData >= 32X There is a 0.27% of reference with a coverageData >= 33X There is a 0.26% of reference with a coverageData >= 34X There is a 0.25% of reference with a coverageData >= 35X There is a 0.24% of reference with a coverageData >= 36X There is a 0.24% of reference with a coverageData >= 37X There is a 0.23% of reference with a coverageData >= 38X There is a 0.22% of reference with a coverageData >= 39X There is a 0.22% of reference with a coverageData >= 40X There is a 0.21% of reference with a coverageData >= 41X There is a 0.2% of reference with a coverageData >= 42X There is a 0.2% of reference with a coverageData >= 43X There is a 0.19% of reference with a coverageData >= 44X There is a 0.18% of reference with a coverageData >= 45X There is a 0.18% of reference with a coverageData >= 46X There is a 0.17% of reference with a coverageData >= 47X There is a 0.17% of reference with a coverageData >= 48X There is a 0.16% of reference with a coverageData >= 49X There is a 0.16% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 192285297 0.7714536326069976 10.241090595666577 chr2 243199373 184137178 0.7571449536590705 7.880571614344007 chr3 198022430 139063236 0.7022600217561212 4.395136446431331 chr4 191154276 146199836 0.7648263960362571 4.777160815261775 chr5 180915260 143155332 0.7912838972234846 4.768163712187331 chr6 171115067 120096769 0.7018480085099695 5.311792252626014 chr7 159138663 127215482 0.799400218663393 9.904391646118828 chr8 146364022 107233897 0.7326520242795733 11.877176392183742 chr9 141213431 90551709 0.6412400602319478 5.85790070751704 chr10 135534747 101173420 0.7464758834131294 6.47511541069191 chr11 135006516 100405347 0.7437074148332218 5.966052567967211 chr12 133851895 94071764 0.7028048725047934 4.474777441685842 chr13 115169878 62620893 0.5437263118399761 3.8358607862035945 chr14 107349540 64663200 0.6023612211100299 4.255024739000221 chr15 102531392 61391559 0.5987586611522839 4.085494490015138 chr16 90354753 59868352 0.6625921715485183 4.208088759603571 chr17 81195210 59464880 0.732369310948269 4.736041317824342 chr18 78077248 56028875 0.7176082205151493 16.191045026361568 chr19 59128983 39992331 0.6763574979803052 7.539140016665947 chr20 63025520 44192826 0.7011893912180336 4.5995703662952465 chr21 48129895 26735825 0.555493108804829 4.281913275644176 chr22 51304566 23001552 0.4483334290363162 4.011476804240694 chrMT 16571 3440478 207.62042121779012 163.4821672111976 chrX 155270560 64978668 0.4184867240769918 3.7874060285709343 chrY 59373566 15594060 0.2626431432466091 3.4087605500399403