BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1954921.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.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 = 15,046,350 number of mapped reads = 14,692,194 (97.65%) number of supplementary alignments = 27,358 (0.18%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,462,574 number of mapped paired reads (second in pair) = 7,229,620 number of mapped paired reads (both in pair) = 14,437,440 number of mapped paired reads (singletons) = 254,754 number of mapped bases = 1,373,950,677 bp number of sequenced bases = 1,373,048,171 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 630,610 duplication rate = 3.62% >>>>>>> Insert size mean insert size = 31,603.4192 std insert size = 1,801,115.2838 median insert size = 356 >>>>>>> Mapping quality mean mapping quality = 54.3286 >>>>>>> ACTG content number of A's = 392,379,680 bp (28.58%) number of C's = 272,716,957 bp (19.86%) number of T's = 392,087,243 bp (28.56%) number of G's = 315,792,623 bp (23%) number of N's = 71,668 bp (0.01%) GC percentage = 42.86% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 11,796,106 number of insertions = 229,565 mapped reads with insertion percentage = 1.54% number of deletions = 655,121 mapped reads with deletion percentage = 4.36% homopolymer indels = 54.26% >>>>>>> Coverage mean coverageData = 0.4438X std coverageData = 1.2961X There is a 23.42% of reference with a coverageData >= 1X There is a 9.75% of reference with a coverageData >= 2X There is a 4.72% of reference with a coverageData >= 3X There is a 2.5% of reference with a coverageData >= 4X There is a 1.41% of reference with a coverageData >= 5X There is a 0.84% of reference with a coverageData >= 6X There is a 0.51% of reference with a coverageData >= 7X There is a 0.32% of reference with a coverageData >= 8X There is a 0.21% of reference with a coverageData >= 9X There is a 0.14% of reference with a coverageData >= 10X There is a 0.1% of reference with a coverageData >= 11X There is a 0.07% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% 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 116748629 0.4683985481424337 1.3792927028313022 chr2 243199373 119430296 0.49107978580191486 2.096361910935687 chr3 198022430 93876524 0.4740701545779435 1.1237920525228027 chr4 191154276 78290481 0.40956698766184024 1.1162751500007997 chr5 180915260 85599849 0.4731488598584774 1.117424868229624 chr6 171115067 77329401 0.45191462304134794 1.1020323682535866 chr7 159138663 69620536 0.43748347942322474 1.0968654560839208 chr8 146364022 71238937 0.486724374108823 1.1966831760455683 chr9 141213431 59392942 0.4205898941723185 1.385007037092354 chr10 135534747 67960288 0.5014233582477562 1.264887954337216 chr11 135006516 67957971 0.5033680818783591 1.2894411622493944 chr12 133851895 63398706 0.47364817659100006 1.1439547621918944 chr13 115169878 40575819 0.3523127722684572 0.9578484538065716 chr14 107349540 63172433 0.5884741844259417 1.4152491193795038 chr15 102531392 40678998 0.39674676415199744 1.063244918326137 chr16 90354753 43392709 0.48024821671528445 1.528336932376275 chr17 81195210 37591604 0.46297809932383943 1.1965560901889514 chr18 78077248 36716539 0.47025913362110305 1.5912166695543355 chr19 59128983 21956415 0.3713308412559709 1.1156968836347467 chr20 63025520 35025259 0.5557313767502434 1.297376506760362 chr21 48129895 18806776 0.3907504057509371 1.4596286967763372 chr22 51304566 18408973 0.35881743936787225 1.0622038423093814 chrMT 16571 206657 12.471003560436907 9.136144082708599 chrX 155270560 39204656 0.2524925265935796 0.7494517766448345 chrY 59373566 7369279 0.12411717025721514 0.7679860844915756