BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173862.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 = 4,826,566 number of mapped reads = 4,708,206 (97.55%) number of supplementary alignments = 436,705 (9.05%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,355,781 number of mapped paired reads (second in pair) = 2,352,425 number of mapped paired reads (both in pair) = 4,632,654 number of mapped paired reads (singletons) = 75,552 number of mapped bases = 555,056,625 bp number of sequenced bases = 554,745,453 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,667,741 duplication rate = 65.17% >>>>>>> Insert size mean insert size = 801,599.9543 std insert size = 8,099,634.9288 median insert size = 197 >>>>>>> Mapping quality mean mapping quality = 52.7587 >>>>>>> ACTG content number of A's = 166,605,301 bp (30.03%) number of C's = 109,339,471 bp (19.71%) number of T's = 166,002,488 bp (29.92%) number of G's = 112,792,055 bp (20.33%) number of N's = 6,138 bp (0%) GC percentage = 40.04% >>>>>>> Mismatches and indels general error rate = 0.0102 number of mismatches = 5,501,225 number of insertions = 58,153 mapped reads with insertion percentage = 1.19% number of deletions = 123,287 mapped reads with deletion percentage = 2.55% homopolymer indels = 43.36% >>>>>>> Coverage mean coverageData = 0.1793X std coverageData = 2.5936X There is a 3.62% of reference with a coverageData >= 1X There is a 2.88% of reference with a coverageData >= 2X There is a 2.25% of reference with a coverageData >= 3X There is a 1.87% of reference with a coverageData >= 4X There is a 1.44% of reference with a coverageData >= 5X There is a 1.17% of reference with a coverageData >= 6X There is a 0.88% of reference with a coverageData >= 7X There is a 0.72% of reference with a coverageData >= 8X There is a 0.53% of reference with a coverageData >= 9X There is a 0.44% of reference with a coverageData >= 10X There is a 0.33% of reference with a coverageData >= 11X There is a 0.28% of reference with a coverageData >= 12X There is a 0.21% of reference with a coverageData >= 13X There is a 0.19% of reference with a coverageData >= 14X There is a 0.14% of reference with a coverageData >= 15X There is a 0.12% of reference with a coverageData >= 16X There is a 0.09% of reference with a coverageData >= 17X There is a 0.08% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% 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 0.01% 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 41724198 0.16739857189764032 1.9499313053503322 chr2 243199373 46940165 0.19301104448159906 7.489562907368316 chr3 198022430 39940468 0.201696686582424 1.3406097284548182 chr4 191154276 26069666 0.1363802398016982 1.280688333801961 chr5 180915260 34876058 0.1927756564039982 1.279110435861498 chr6 171115067 30321396 0.17719886700567403 1.3990392426506848 chr7 159138663 33986329 0.21356424868292379 1.861190460810553 chr8 146364022 35440458 0.242139137171292 2.121727211194434 chr9 141213431 21398529 0.15153324190529724 1.3342366074273249 chr10 135534747 24351470 0.1796695721134891 2.531453771138225 chr11 135006516 20509963 0.15191831926097552 1.149167400261248 chr12 133851895 26577419 0.19855840666282684 1.3143309632791917 chr13 115169878 13332570 0.11576438415607247 0.9932715786130462 chr14 107349540 17518893 0.1631948585899856 1.1741238031388297 chr15 102531392 19518710 0.19036813622895124 1.277726379207421 chr16 90354753 18814118 0.20822499509239983 1.6554871424719952 chr17 81195210 23259398 0.28646268665356 1.6909802830671787 chr18 78077248 10770366 0.1379450003155849 1.9465184560234565 chr19 59128983 9299759 0.1572791975806518 1.5796037877071707 chr20 63025520 25296662 0.4013717300547461 2.0285990088017463 chr21 48129895 6991129 0.14525543843384658 1.1741613260972559 chr22 51304566 4135877 0.08061420887957614 0.7925414913142158 chrMT 16571 1691282 102.0627602437994 77.72474584207431 chrX 155270560 21311602 0.13725462186779 1.0843077095430291 chrY 59373566 980140 0.016508019747373773 0.5978365178252296