BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173992.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 4,896,774 number of mapped reads = 4,787,355 (97.77%) number of supplementary alignments = 606,228 (12.38%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,394,221 number of mapped paired reads (second in pair) = 2,393,134 number of mapped paired reads (both in pair) = 4,718,462 number of mapped paired reads (singletons) = 68,893 number of mapped bases = 544,378,753 bp number of sequenced bases = 544,022,984 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,800,193 duplication rate = 64.5% >>>>>>> Insert size mean insert size = 846,752.4562 std insert size = 8,840,813.4208 median insert size = 157 >>>>>>> Mapping quality mean mapping quality = 52.5783 >>>>>>> ACTG content number of A's = 161,695,132 bp (29.72%) number of C's = 108,919,177 bp (20.02%) number of T's = 160,344,270 bp (29.47%) number of G's = 113,059,949 bp (20.78%) number of N's = 4,456 bp (0%) GC percentage = 40.8% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 4,643,853 number of insertions = 60,288 mapped reads with insertion percentage = 1.21% number of deletions = 147,508 mapped reads with deletion percentage = 3.01% homopolymer indels = 41.49% >>>>>>> Coverage mean coverageData = 0.1759X std coverageData = 3.1011X There is a 3.82% of reference with a coverageData >= 1X There is a 2.86% of reference with a coverageData >= 2X There is a 2.13% of reference with a coverageData >= 3X There is a 1.71% of reference with a coverageData >= 4X There is a 1.28% of reference with a coverageData >= 5X There is a 1.06% of reference with a coverageData >= 6X There is a 0.79% of reference with a coverageData >= 7X There is a 0.68% of reference with a coverageData >= 8X There is a 0.5% of reference with a coverageData >= 9X There is a 0.45% of reference with a coverageData >= 10X There is a 0.33% of reference with a coverageData >= 11X There is a 0.31% of reference with a coverageData >= 12X There is a 0.22% of reference with a coverageData >= 13X There is a 0.21% of reference with a coverageData >= 14X There is a 0.15% of reference with a coverageData >= 15X There is a 0.14% of reference with a coverageData >= 16X There is a 0.1% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.05% 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 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% 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% 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 43660563 0.1751673188409027 1.91373220448401 chr2 243199373 47009185 0.19329484455537638 9.719574837791436 chr3 198022430 36820167 0.185939375655576 1.289329638792425 chr4 191154276 35455761 0.18548243723305463 1.651005799511259 chr5 180915260 34735778 0.19200026575978169 1.3144535194933424 chr6 171115067 32611708 0.19058349782839404 1.5146402900872857 chr7 159138663 30006413 0.1885551407454014 1.6086108333322535 chr8 146364022 28145551 0.1922982889879864 1.887160409122015 chr9 141213431 23079378 0.16343613944200533 1.6192781180940758 chr10 135534747 25601711 0.18889407747225145 2.008537424533959 chr11 135006516 26113145 0.19342136789901312 1.3626139050692425 chr12 133851895 26545617 0.19832081570455165 1.3694459030826605 chr13 115169878 17309174 0.1502925443751881 1.1613750903456335 chr14 107349540 16640792 0.15501502847613507 1.1898675066398685 chr15 102531392 14838373 0.14472029210331994 1.146159564915872 chr16 90354753 17063108 0.18884571573119124 1.5488609415526753 chr17 81195210 15084067 0.18577533083540274 1.3902165494753198 chr18 78077248 15446958 0.19784198848811885 2.335890148890931 chr19 59128983 11470931 0.19399844911927538 1.601786580748094 chr20 63025520 12411812 0.1969331153475608 1.3993444219075934 chr21 48129895 7990979 0.16602942931830622 1.4600476415788197 chr22 51304566 7322310 0.1427223845924357 1.2399228480259457 chrMT 16571 819956 49.48138313921912 43.35500991407807 chrX 155270560 14049008 0.0904808226363066 0.8956777133640512 chrY 59373566 4146308 0.06983424239669216 1.14852897898232