BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927062.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 31,243,586 number of mapped reads = 30,423,938 (97.38%) number of supplementary alignments = 1,024,273 (3.28%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,270,343 number of mapped paired reads (second in pair) = 15,153,595 number of mapped paired reads (both in pair) = 29,993,038 number of mapped paired reads (singletons) = 430,900 number of mapped bases = 2,800,395,134 bp number of sequenced bases = 2,798,288,151 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,827,214 duplication rate = 7.48% >>>>>>> Insert size mean insert size = 334,969.378 std insert size = 5,717,020.0222 median insert size = 176 >>>>>>> Mapping quality mean mapping quality = 52.8152 >>>>>>> ACTG content number of A's = 790,667,297 bp (28.26%) number of C's = 562,134,520 bp (20.09%) number of T's = 799,923,309 bp (28.59%) number of G's = 645,372,022 bp (23.06%) number of N's = 191,003 bp (0.01%) GC percentage = 43.15% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 26,272,111 number of insertions = 477,103 mapped reads with insertion percentage = 1.54% number of deletions = 1,426,974 mapped reads with deletion percentage = 4.57% homopolymer indels = 51.84% >>>>>>> Coverage mean coverageData = 0.9046X std coverageData = 2.9705X There is a 34.43% of reference with a coverageData >= 1X There is a 19.72% of reference with a coverageData >= 2X There is a 11.63% of reference with a coverageData >= 3X There is a 7.36% of reference with a coverageData >= 4X There is a 4.8% of reference with a coverageData >= 5X There is a 3.23% of reference with a coverageData >= 6X There is a 2.22% of reference with a coverageData >= 7X There is a 1.56% of reference with a coverageData >= 8X There is a 1.11% of reference with a coverageData >= 9X There is a 0.81% of reference with a coverageData >= 10X There is a 0.59% of reference with a coverageData >= 11X There is a 0.44% of reference with a coverageData >= 12X There is a 0.33% of reference with a coverageData >= 13X There is a 0.25% of reference with a coverageData >= 14X There is a 0.19% of reference with a coverageData >= 15X There is a 0.15% of reference with a coverageData >= 16X There is a 0.12% of reference with a coverageData >= 17X There is a 0.09% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.05% 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 0.03% 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 0.01% 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 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% 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 232131064 0.9313158902821751 2.8811980479158152 chr2 243199373 245752171 1.010496729364512 5.324609777093696 chr3 198022430 183966018 0.9290160614633403 1.899323027671335 chr4 191154276 153864613 0.8049237308193933 2.2292029413982646 chr5 180915260 161770808 0.8941800044949221 1.8604798216590024 chr6 171115067 153600191 0.8976427014460392 1.8850036601293771 chr7 159138663 141987336 0.8922240096990133 2.1387114478782685 chr8 146364022 134355015 0.9179511000319464 2.0226863338091197 chr9 141213431 129099045 0.9142122253229581 3.071078352425513 chr10 135534747 140358989 1.0355941343956616 3.9728600203292497 chr11 135006516 136837974 1.0135657007843977 2.422934996418769 chr12 133851895 128343176 0.958844669326497 2.147943347381406 chr13 115169878 76541643 0.6645977605359623 1.62908564264082 chr14 107349540 85910505 0.8002875932211726 1.8579298598757426 chr15 102531392 90716634 0.884769359222198 1.9579727884187204 chr16 90354753 93116399 1.030564479546527 3.8941703039036035 chr17 81195210 80225701 0.9880595296200355 2.1682582989971952 chr18 78077248 72776622 0.9321104913943689 3.0256648029410824 chr19 59128983 51330489 0.8681104662327779 2.26250874796886 chr20 63025520 70428013 1.1174523113811674 2.2595931785089984 chr21 48129895 35701051 0.7417645727255379 2.569031007435911 chr22 51304566 40633039 0.7919965447129989 2.0068300925739764 chrMT 16571 5984184 361.12389113511557 273.98462498850307 chrX 155270560 150272883 0.9678131063609225 2.031476463491981 chrY 59373566 4691571 0.07901784103720501 2.7881775908640307