BamQC report ----------------------------------- >>>>>>> Input bam file = SRR22354856.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP408873/SRP408873.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 = 22,187,246 number of mapped reads = 21,245,465 (95.76%) number of supplementary alignments = 329,760 (1.49%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,643,415 number of mapped paired reads (second in pair) = 10,602,050 number of mapped paired reads (both in pair) = 21,180,364 number of mapped paired reads (singletons) = 65,101 number of mapped bases = 2,964,749,160 bp number of sequenced bases = 2,963,400,507 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 19,403,787 duplication rate = 84.68% >>>>>>> Insert size mean insert size = 119,718.2343 std insert size = 3,866,824.254 median insert size = 249 >>>>>>> Mapping quality mean mapping quality = 54.1938 >>>>>>> ACTG content number of A's = 849,686,769 bp (28.67%) number of C's = 623,667,297 bp (21.05%) number of T's = 855,385,087 bp (28.86%) number of G's = 634,646,492 bp (21.42%) number of N's = 14,862 bp (0%) GC percentage = 42.46% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 19,101,300 number of insertions = 446,344 mapped reads with insertion percentage = 1.95% number of deletions = 482,838 mapped reads with deletion percentage = 2.17% homopolymer indels = 44.2% >>>>>>> Coverage mean coverageData = 0.9577X std coverageData = 23.3228X There is a 6.3% of reference with a coverageData >= 1X There is a 5.99% of reference with a coverageData >= 2X There is a 5.61% of reference with a coverageData >= 3X There is a 5.42% of reference with a coverageData >= 4X There is a 5.09% of reference with a coverageData >= 5X There is a 4.9% of reference with a coverageData >= 6X There is a 4.55% of reference with a coverageData >= 7X There is a 4.34% of reference with a coverageData >= 8X There is a 3.98% of reference with a coverageData >= 9X There is a 3.76% of reference with a coverageData >= 10X There is a 3.42% of reference with a coverageData >= 11X There is a 3.21% of reference with a coverageData >= 12X There is a 2.89% of reference with a coverageData >= 13X There is a 2.7% of reference with a coverageData >= 14X There is a 2.42% of reference with a coverageData >= 15X There is a 2.26% of reference with a coverageData >= 16X There is a 2.02% of reference with a coverageData >= 17X There is a 1.88% of reference with a coverageData >= 18X There is a 1.68% of reference with a coverageData >= 19X There is a 1.57% of reference with a coverageData >= 20X There is a 1.39% of reference with a coverageData >= 21X There is a 1.29% of reference with a coverageData >= 22X There is a 1.14% of reference with a coverageData >= 23X There is a 1.06% of reference with a coverageData >= 24X There is a 0.93% of reference with a coverageData >= 25X There is a 0.86% of reference with a coverageData >= 26X There is a 0.75% of reference with a coverageData >= 27X There is a 0.7% of reference with a coverageData >= 28X There is a 0.61% of reference with a coverageData >= 29X There is a 0.57% of reference with a coverageData >= 30X There is a 0.49% of reference with a coverageData >= 31X There is a 0.46% of reference with a coverageData >= 32X There is a 0.4% of reference with a coverageData >= 33X There is a 0.37% of reference with a coverageData >= 34X There is a 0.32% of reference with a coverageData >= 35X There is a 0.3% of reference with a coverageData >= 36X There is a 0.26% of reference with a coverageData >= 37X There is a 0.25% of reference with a coverageData >= 38X There is a 0.22% of reference with a coverageData >= 39X There is a 0.21% of reference with a coverageData >= 40X There is a 0.18% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.14% of reference with a coverageData >= 43X There is a 0.14% of reference with a coverageData >= 44X There is a 0.12% of reference with a coverageData >= 45X There is a 0.11% of reference with a coverageData >= 46X There is a 0.1% of reference with a coverageData >= 47X There is a 0.09% of reference with a coverageData >= 48X There is a 0.08% of reference with a coverageData >= 49X There is a 0.08% of reference with a coverageData >= 50X There is a 0.07% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 212245937 0.8515362415085016 25.748048585319506 chr2 243199373 246090463 1.0118877362401753 47.54461098021882 chr3 198022430 192208004 0.9706375383839093 4.6191063879519065 chr4 191154276 184357406 0.9644430135583261 15.314580370335209 chr5 180915260 161527370 0.892834413194332 4.382433437684002 chr6 171115067 173202658 1.0121999250948486 6.050375673538949 chr7 159138663 144979340 0.9110252484652331 10.995931250040405 chr8 146364022 162536998 1.1104983026498139 5.949995519784514 chr9 141213431 146407452 1.036781352617939 15.727453426589731 chr10 135534747 161799793 1.1937882836790186 24.334342938453265 chr11 135006516 128551145 0.9521847449200156 6.03306418989133 chr12 133851895 122052970 0.9118508931083867 4.470594509165562 chr13 115169878 91836138 0.7973971979027363 4.15378974817433 chr14 107349540 90626331 0.844217227200042 4.61488627528355 chr15 102531392 72724416 0.709289268207731 3.872606798004598 chr16 90354753 93593574 1.035845607369432 6.699735578242742 chr17 81195210 80108664 0.9866181022254884 6.888871491311438 chr18 78077248 94597733 1.2115915381648696 14.77046778993403 chr19 59128983 59990342 1.0145674583985318 13.88403984484892 chr20 63025520 58667170 0.930847853377489 6.77509596522078 chr21 48129895 39395900 0.8185328474121957 9.065181511984033 chr22 51304566 34892526 0.6801056654489583 4.70496067147686 chrMT 16571 106228189 6410.487538470822 983.9181502162971 chrX 155270560 72475910 0.46677174346508443 3.512194105153896 chrY 59373566 33652731 0.566796526925804 15.392908024831842