BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695929.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 = 97,216,660 number of mapped reads = 86,186,774 (88.65%) number of supplementary alignments = 2,360,173 (2.43%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 45,333,651 number of mapped paired reads (second in pair) = 40,853,123 number of mapped paired reads (both in pair) = 78,938,826 number of mapped paired reads (singletons) = 7,247,948 number of mapped bases = 7,253,124,409 bp number of sequenced bases = 7,250,194,273 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 54,372,223 duplication rate = 30.11% >>>>>>> Insert size mean insert size = 136,178.0472 std insert size = 3,529,835.8389 median insert size = 321 >>>>>>> Mapping quality mean mapping quality = 51.7985 >>>>>>> ACTG content number of A's = 1,892,874,920 bp (26.11%) number of C's = 1,323,438,397 bp (18.25%) number of T's = 2,331,339,357 bp (32.16%) number of G's = 1,673,430,411 bp (23.08%) number of N's = 29,111,188 bp (0.4%) GC percentage = 41.34% >>>>>>> Mismatches and indels general error rate = 0.0158 number of mismatches = 113,615,511 number of insertions = 591,895 mapped reads with insertion percentage = 0.68% number of deletions = 1,660,006 mapped reads with deletion percentage = 1.9% homopolymer indels = 46.73% >>>>>>> Coverage mean coverageData = 2.343X std coverageData = 21.2865X There is a 20.3% of reference with a coverageData >= 1X There is a 14.48% of reference with a coverageData >= 2X There is a 11.54% of reference with a coverageData >= 3X There is a 9.85% of reference with a coverageData >= 4X There is a 8.68% of reference with a coverageData >= 5X There is a 7.82% of reference with a coverageData >= 6X There is a 7.15% of reference with a coverageData >= 7X There is a 6.61% of reference with a coverageData >= 8X There is a 6.15% of reference with a coverageData >= 9X There is a 5.75% of reference with a coverageData >= 10X There is a 5.4% of reference with a coverageData >= 11X There is a 5.09% of reference with a coverageData >= 12X There is a 4.81% of reference with a coverageData >= 13X There is a 4.56% of reference with a coverageData >= 14X There is a 4.32% of reference with a coverageData >= 15X There is a 4.1% of reference with a coverageData >= 16X There is a 3.9% of reference with a coverageData >= 17X There is a 3.7% of reference with a coverageData >= 18X There is a 3.52% of reference with a coverageData >= 19X There is a 3.36% of reference with a coverageData >= 20X There is a 3.2% of reference with a coverageData >= 21X There is a 3.05% of reference with a coverageData >= 22X There is a 2.91% of reference with a coverageData >= 23X There is a 2.77% of reference with a coverageData >= 24X There is a 2.65% of reference with a coverageData >= 25X There is a 2.53% of reference with a coverageData >= 26X There is a 2.41% of reference with a coverageData >= 27X There is a 2.3% of reference with a coverageData >= 28X There is a 2.2% of reference with a coverageData >= 29X There is a 2.1% of reference with a coverageData >= 30X There is a 2.01% of reference with a coverageData >= 31X There is a 1.92% of reference with a coverageData >= 32X There is a 1.83% of reference with a coverageData >= 33X There is a 1.75% of reference with a coverageData >= 34X There is a 1.67% of reference with a coverageData >= 35X There is a 1.6% of reference with a coverageData >= 36X There is a 1.53% of reference with a coverageData >= 37X There is a 1.46% of reference with a coverageData >= 38X There is a 1.4% of reference with a coverageData >= 39X There is a 1.34% of reference with a coverageData >= 40X There is a 1.28% of reference with a coverageData >= 41X There is a 1.23% of reference with a coverageData >= 42X There is a 1.18% of reference with a coverageData >= 43X There is a 1.13% of reference with a coverageData >= 44X There is a 1.08% of reference with a coverageData >= 45X There is a 1.03% of reference with a coverageData >= 46X There is a 0.99% of reference with a coverageData >= 47X There is a 0.95% of reference with a coverageData >= 48X There is a 0.91% of reference with a coverageData >= 49X There is a 0.88% of reference with a coverageData >= 50X There is a 0.84% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 659624350 2.6464301166174424 35.85808761405656 chr2 243199373 626528657 2.576193553755585 24.383699521552483 chr3 198022430 472150970 2.384330754854387 11.290621533439984 chr4 191154276 492354782 2.5756932688233456 12.475356098743251 chr5 180915260 485114565 2.68144635781415 12.132139036452774 chr6 171115067 407484823 2.3813497557173036 15.365584359134774 chr7 159138663 434085455 2.727718373504244 27.72113114066372 chr8 146364022 365246572 2.4954668982791413 37.684526755280274 chr9 141213431 307860967 2.180111090141277 18.166892161016428 chr10 135534747 345883262 2.5519895794692413 19.710440802175903 chr11 135006516 342046327 2.5335542100797563 18.22459500299411 chr12 133851895 320451589 2.3940758477868394 11.709846121569589 chr13 115169878 212391577 1.8441590864583532 9.94903881956811 chr14 107349540 219327251 2.0431130957803827 11.181683399874126 chr15 102531392 209095120 2.039327818742576 10.512037196334527 chr16 90354753 208457884 2.3071047961361812 11.628252790081335 chr17 81195210 207953488 2.5611546296881307 13.580531864798102 chr18 78077248 189140234 2.4224756743475386 46.40721347027578 chr19 59128983 140057710 2.3686811931130287 23.469867101453968 chr20 63025520 152720599 2.423154922006197 12.400569484399782 chr21 48129895 91951882 1.9104941325967988 11.973538976793783 chr22 51304566 79623725 1.5519812603034202 11.10222992532189 chrMT 16571 11200106 675.8859453261722 475.64986288497647 chrX 155270560 217156018 1.3985653043307116 10.216372433933072 chrY 59373566 55216496 0.929984498488772 11.66965540287309