BamQC report ----------------------------------- >>>>>>> Input bam file = SRR22354879.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP408873/SRP408873.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 = 19,739,416 number of mapped reads = 19,598,673 (99.29%) number of supplementary alignments = 461,101 (2.34%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,808,312 number of mapped paired reads (second in pair) = 9,790,361 number of mapped paired reads (both in pair) = 19,560,192 number of mapped paired reads (singletons) = 38,481 number of mapped bases = 2,596,660,672 bp number of sequenced bases = 2,595,219,908 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,032,613 duplication rate = 33.81% >>>>>>> Insert size mean insert size = 212,405.3591 std insert size = 5,277,993.3116 median insert size = 191 >>>>>>> Mapping quality mean mapping quality = 54.019 >>>>>>> ACTG content number of A's = 744,891,273 bp (28.7%) number of C's = 540,524,431 bp (20.83%) number of T's = 751,537,228 bp (28.96%) number of G's = 558,255,032 bp (21.51%) number of N's = 11,944 bp (0%) GC percentage = 42.34% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 19,165,391 number of insertions = 491,772 mapped reads with insertion percentage = 2.34% number of deletions = 513,577 mapped reads with deletion percentage = 2.49% homopolymer indels = 44.36% >>>>>>> Coverage mean coverageData = 0.8388X std coverageData = 20.4806X There is a 35.51% of reference with a coverageData >= 1X There is a 22.41% of reference with a coverageData >= 2X There is a 9.45% of reference with a coverageData >= 3X There is a 5.89% of reference with a coverageData >= 4X There is a 2.48% of reference with a coverageData >= 5X There is a 1.53% of reference with a coverageData >= 6X There is a 0.67% of reference with a coverageData >= 7X There is a 0.41% of reference with a coverageData >= 8X There is a 0.2% of reference with a coverageData >= 9X There is a 0.13% of reference with a coverageData >= 10X There is a 0.08% of reference with a coverageData >= 11X There is a 0.06% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% 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 0.02% 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 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 211327956 0.8478532777657553 23.37886790164419 chr2 243199373 235425471 0.968034860024084 61.406881222170234 chr3 198022430 170750286 0.862277500584151 1.8001161108606558 chr4 191154276 176747051 0.924630380750677 12.511247448642882 chr5 180915260 156128071 0.8629900595450046 1.5239506076860299 chr6 171115067 147804646 0.8637734162825066 3.4952064117083363 chr7 159138663 141963930 0.8920769304188512 12.769427563597146 chr8 146364022 127954164 0.8742186928970836 3.543698144519489 chr9 141213431 111304440 0.7882000969157105 13.03533858802024 chr10 135534747 143713458 1.0603440164314468 28.317211636201655 chr11 135006516 117990265 0.8739597798375894 4.439976282832113 chr12 133851895 114073291 0.8522351588671943 1.5284948928287916 chr13 115169878 81987315 0.7118815824394639 1.344458511861634 chr14 107349540 78088594 0.7274236480193581 3.4072778530207533 chr15 102531392 73637290 0.7181926292388578 1.3484675238958093 chr16 90354753 79464411 0.8794712880239958 5.592339498776219 chr17 81195210 71691381 0.8829508661902592 5.121096617075372 chr18 78077248 71508958 0.9158744683214245 10.711115850348122 chr19 59128983 51277573 0.8672155413192207 11.604525898253275 chr20 63025520 53996996 0.8567481236172269 4.196720617148492 chr21 48129895 36368813 0.7556387355509502 6.384959234771491 chr22 51304566 31044544 0.6051029454181525 2.6301334566947228 chrMT 16571 11368304 686.0360871401847 127.63326662610811 chrX 155270560 70153832 0.45181669983028333 1.8282753170364077 chrY 59373566 30889632 0.5202589987604922 14.874332033647804