BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038498.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 17,413,106 number of mapped reads = 15,488,491 (88.95%) number of supplementary alignments = 271,424 (1.56%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,869,137 number of mapped paired reads (second in pair) = 7,619,354 number of mapped paired reads (both in pair) = 15,181,028 number of mapped paired reads (singletons) = 307,463 number of mapped bases = 2,063,513,202 bp number of sequenced bases = 2,062,061,485 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,642,187 duplication rate = 16.06% >>>>>>> Insert size mean insert size = 87,684.6001 std insert size = 2,891,219.0813 median insert size = 243 >>>>>>> Mapping quality mean mapping quality = 53.1941 >>>>>>> ACTG content number of A's = 584,590,129 bp (28.35%) number of C's = 413,288,101 bp (20.04%) number of T's = 594,359,582 bp (28.82%) number of G's = 469,660,432 bp (22.78%) number of N's = 163,241 bp (0.01%) GC percentage = 42.82% >>>>>>> Mismatches and indels general error rate = 0.0133 number of mismatches = 26,372,184 number of insertions = 374,793 mapped reads with insertion percentage = 2.29% number of deletions = 720,478 mapped reads with deletion percentage = 4.48% homopolymer indels = 47.33% >>>>>>> Coverage mean coverageData = 0.6666X std coverageData = 10.905X There is a 23.5% of reference with a coverageData >= 1X There is a 13.95% of reference with a coverageData >= 2X There is a 8.2% of reference with a coverageData >= 3X There is a 5.29% of reference with a coverageData >= 4X There is a 3.4% of reference with a coverageData >= 5X There is a 2.28% of reference with a coverageData >= 6X There is a 1.55% of reference with a coverageData >= 7X There is a 1.07% of reference with a coverageData >= 8X There is a 0.75% of reference with a coverageData >= 9X There is a 0.54% of reference with a coverageData >= 10X There is a 0.39% of reference with a coverageData >= 11X There is a 0.29% of reference with a coverageData >= 12X There is a 0.22% of reference with a coverageData >= 13X There is a 0.17% of reference with a coverageData >= 14X There is a 0.13% of reference with a coverageData >= 15X There is a 0.1% of reference with a coverageData >= 16X There is a 0.08% of reference with a coverageData >= 17X There is a 0.07% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% 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 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 177597494 0.7125257834362627 13.265740435234973 chr2 243199373 183071890 0.7527646463134591 11.77714963278838 chr3 198022430 151554602 0.7653405828824543 1.9547246102505205 chr4 191154276 89729217 0.46940732311946815 12.350361588603738 chr5 180915260 136950777 0.756988531536809 1.7877666139548978 chr6 171115067 116476510 0.6806911398398365 8.083488233719569 chr7 159138663 97457367 0.6124053398638897 10.32144902217605 chr8 146364022 127676359 0.8723206513141597 3.962653615742076 chr9 141213431 86635194 0.6135053400125942 16.62333722847947 chr10 135534747 115507502 0.8522353459663005 30.782887934837024 chr11 135006516 88262272 0.6537630524440761 7.604231021513133 chr12 133851895 83348917 0.6226950839956357 1.733213684874254 chr13 115169878 64616152 0.5610507983693445 1.480482161374939 chr14 107349540 65320009 0.6084796357767346 1.653668338814162 chr15 102531392 76153028 0.7427289000426328 1.8748234235695793 chr16 90354753 76046863 0.8416476220127568 9.80067482362514 chr17 81195210 52477311 0.6463104289033799 13.231646840146531 chr18 78077248 81747035 1.0470020024271347 12.44629411878363 chr19 59128983 26620077 0.4502035321662813 5.66960677193452 chr20 63025520 55341110 0.8780746275476982 4.385891199134884 chr21 48129895 19743484 0.4102124885167524 5.4783610866216215 chr22 51304566 11709144 0.22822810741640423 0.9762992735962144 chrMT 16571 6278755 378.90018707380364 228.70407785631818 chrX 155270560 68129044 0.4387763140675219 2.1370239443779644 chrY 59373566 5063089 0.08527513742395058 12.598058540990603