BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124791.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 = 575,108 number of mapped reads = 574,415 (99.88%) number of supplementary alignments = 254,910 (44.32%) number of secondary alignments = 0 number of mapped bases = 85,822,044 bp number of sequenced bases = 85,786,922 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 826,994 duplication rate = 21.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.617 >>>>>>> ACTG content number of A's = 22,811,896 bp (26.59%) number of C's = 16,768,161 bp (19.55%) number of T's = 27,637,108 bp (32.22%) number of G's = 18,569,757 bp (21.65%) number of N's = 0 bp (0%) GC percentage = 41.19% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 683,279 number of insertions = 20,091 mapped reads with insertion percentage = 3.47% number of deletions = 33,289 mapped reads with deletion percentage = 5.63% homopolymer indels = 82.63% >>>>>>> Coverage mean coverageData = 0.0277X std coverageData = 61.6689X There is a 0.01% 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 95269 3.822217157083833E-4 0.2765874078017744 chr2 243199373 19982 8.216304077395792E-5 0.009211383755650476 chr3 198022430 20218 1.0209954498588872E-4 0.04642260857662992 chr4 191154276 10755 5.626345496974391E-5 0.007551083963093242 chr5 180915260 10884 6.0160762558116986E-5 0.007765362982732393 chr6 171115067 16159 9.443353109285227E-5 0.014197701818581241 chr7 159138663 12119 7.615371256449478E-5 0.0099616616738379 chr8 146364022 83507358 0.5705456631958364 283.4531163270127 chr9 141213431 9970 7.060234943232844E-5 0.008401381063949942 chr10 135534747 2021347 0.014913865593448152 9.905867478135171 chr11 135006516 11510 8.52551442776288E-5 0.009229367462386723 chr12 133851895 9834 7.346926242620622E-5 0.008575899402719184 chr13 115169878 6034 5.2392171501649066E-5 0.007354085962420297 chr14 107349540 7819 7.283682817830426E-5 0.009489273821871445 chr15 102531392 8629 8.41595908499906E-5 0.015659977170347426 chr16 90354753 6159 6.81646487374051E-5 0.00826863266014942 chr17 81195210 6134 7.554632841025966E-5 0.008936640203751263 chr18 78077248 3588 4.595448855984268E-5 0.006778818241022833 chr19 59128983 17320 2.929189565124095E-4 0.09708263641229146 chr20 63025520 5785 9.17882153134159E-5 0.009580176941839096 chr21 48129895 1795 3.729490787378614E-5 0.0061051405721689045 chr22 51304566 1576 3.071851343601659E-5 0.005584385770145354 chrMT 16571 384 0.023173013095166253 0.15045273197671588 chrX 155270560 9218 5.936733917878573E-5 0.007701865842393201 chrY 59373566 2198 3.70198414560446E-5 0.006297837256249196