BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173985.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 = 2,844,084 number of mapped reads = 2,760,564 (97.06%) number of supplementary alignments = 274,576 (9.65%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,383,396 number of mapped paired reads (second in pair) = 1,377,168 number of mapped paired reads (both in pair) = 2,706,166 number of mapped paired reads (singletons) = 54,398 number of mapped bases = 325,477,414 bp number of sequenced bases = 325,279,932 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,151,537 duplication rate = 64.29% >>>>>>> Insert size mean insert size = 962,796.5008 std insert size = 9,229,434.561 median insert size = 204 >>>>>>> Mapping quality mean mapping quality = 52.7012 >>>>>>> ACTG content number of A's = 97,589,944 bp (30%) number of C's = 64,036,512 bp (19.69%) number of T's = 97,325,007 bp (29.92%) number of G's = 66,324,720 bp (20.39%) number of N's = 3,749 bp (0%) GC percentage = 40.08% >>>>>>> Mismatches and indels general error rate = 0.0109 number of mismatches = 3,458,685 number of insertions = 34,061 mapped reads with insertion percentage = 1.2% number of deletions = 76,351 mapped reads with deletion percentage = 2.7% homopolymer indels = 42.58% >>>>>>> Coverage mean coverageData = 0.1051X std coverageData = 1.6794X There is a 2.18% of reference with a coverageData >= 1X There is a 1.72% of reference with a coverageData >= 2X There is a 1.34% of reference with a coverageData >= 3X There is a 1.11% of reference with a coverageData >= 4X There is a 0.85% of reference with a coverageData >= 5X There is a 0.69% of reference with a coverageData >= 6X There is a 0.51% of reference with a coverageData >= 7X There is a 0.41% of reference with a coverageData >= 8X There is a 0.3% of reference with a coverageData >= 9X There is a 0.25% of reference with a coverageData >= 10X There is a 0.18% of reference with a coverageData >= 11X There is a 0.16% of reference with a coverageData >= 12X There is a 0.11% of reference with a coverageData >= 13X There is a 0.1% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.07% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% 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% 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 28943814 0.11612333756231645 1.3078386827522603 chr2 243199373 34280853 0.14095781817661182 4.575365400860678 chr3 198022430 23540111 0.11887598288739311 1.0099174932313169 chr4 191154276 19889037 0.10404704208657095 1.0744959857819296 chr5 180915260 18379933 0.10159415518624576 0.9228111857106474 chr6 171115067 17903281 0.10462714542840346 0.9588784705773685 chr7 159138663 25391469 0.15955562602659293 1.63048295372993 chr8 146364022 13839932 0.09455829247436232 1.108573415831475 chr9 141213431 13174650 0.09329601233185815 1.0009989903194811 chr10 135534747 12786028 0.09433763874587821 1.7062303366135807 chr11 135006516 14494491 0.10736141802222346 0.9600223326107656 chr12 133851895 12605539 0.09417527484388623 0.8888004274209684 chr13 115169878 9515424 0.0826207699898753 0.8365546179763429 chr14 107349540 7971471 0.074257150985463 0.785951806815734 chr15 102531392 11281798 0.11003262298438317 0.9540790057255407 chr16 90354753 12646635 0.1399664608678638 1.3848873078999224 chr17 81195210 7728127 0.09517959249073929 0.9460913352964692 chr18 78077248 5296748 0.06783983984681427 1.202942585453915 chr19 59128983 5897959 0.0997473438702641 1.3633892127507727 chr20 63025520 9456188 0.15003744514920306 1.1217695852334082 chr21 48129895 4964067 0.10313895345086459 0.9415130724763499 chr22 51304566 2773216 0.054053980302649865 0.6357475947063865 chrMT 16571 1243400 75.03469917325448 60.05534511854132 chrX 155270560 10938566 0.0704484224182614 0.7708782274218473 chrY 59373566 534677 0.00900530380809534 0.4330454249773878