BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927009.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 = 22,971,152 number of mapped reads = 22,367,101 (97.37%) number of supplementary alignments = 379,982 (1.65%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 11,198,766 number of mapped paired reads (second in pair) = 11,168,335 number of mapped paired reads (both in pair) = 21,975,406 number of mapped paired reads (singletons) = 391,695 number of mapped bases = 2,063,499,497 bp number of sequenced bases = 2,061,894,949 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,742,691 duplication rate = 6.12% >>>>>>> Insert size mean insert size = 213,721.1093 std insert size = 4,508,361.6829 median insert size = 247 >>>>>>> Mapping quality mean mapping quality = 51.8194 >>>>>>> ACTG content number of A's = 601,404,170 bp (29.17%) number of C's = 388,694,270 bp (18.85%) number of T's = 614,223,490 bp (29.79%) number of G's = 457,186,912 bp (22.17%) number of N's = 386,107 bp (0.02%) GC percentage = 41.02% >>>>>>> Mismatches and indels general error rate = 0.0102 number of mismatches = 20,428,814 number of insertions = 352,142 mapped reads with insertion percentage = 1.55% number of deletions = 1,130,831 mapped reads with deletion percentage = 4.92% homopolymer indels = 53.07% >>>>>>> Coverage mean coverageData = 0.6666X std coverageData = 2.6336X There is a 30.03% of reference with a coverageData >= 1X There is a 15.23% of reference with a coverageData >= 2X There is a 8.26% of reference with a coverageData >= 3X There is a 4.71% of reference with a coverageData >= 4X There is a 2.78% of reference with a coverageData >= 5X There is a 1.68% of reference with a coverageData >= 6X There is a 1.04% of reference with a coverageData >= 7X There is a 0.65% of reference with a coverageData >= 8X There is a 0.42% of reference with a coverageData >= 9X There is a 0.27% of reference with a coverageData >= 10X There is a 0.18% of reference with a coverageData >= 11X There is a 0.12% of reference with a coverageData >= 12X There is a 0.08% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.04% 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 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% 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 0.01% 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 0.01% 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% 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 173207728 0.6949139276166537 3.6873853786247515 chr2 243199373 187275851 0.7700507147277884 4.214908724155349 chr3 198022430 149962841 0.7573022965125719 1.4956612260432878 chr4 191154276 141270850 0.7390410141806087 1.8899212824948868 chr5 180915260 134963664 0.7460048643768359 1.4823637925526065 chr6 171115067 127556102 0.7454405052478518 2.444957328828618 chr7 159138663 113173448 0.7111624910409107 2.2328082815566543 chr8 146364022 113278708 0.7739518663951446 1.754889970060086 chr9 141213431 91077433 0.6449629638982428 3.192112372618144 chr10 135534747 104051333 0.7677096486556322 5.128011788637141 chr11 135006516 102756714 0.7611241075208548 2.396242994091356 chr12 133851895 1976793 0.014768509627749386 0.30567180122884335 chr13 115169878 68598868 0.5956320280203822 1.3237135394380986 chr14 107349540 65237494 0.6077109785472765 1.3895998312926465 chr15 102531392 62299462 0.6076135394709163 1.3931187786824712 chr16 90354753 61277785 0.6781910521076849 3.2700864822668416 chr17 81195210 49938618 0.6150438923675424 1.6895093994100652 chr18 78077248 57969391 0.7424620165915684 3.068156703978972 chr19 59128983 28726245 0.48582342436026676 2.4764151214343335 chr20 63025520 46985769 0.7455038689089752 1.5936788856904196 chr21 48129895 26310520 0.5466565011205613 2.129093923378374 chr22 51304566 23745731 0.46283855125097445 1.2395799843616149 chrMT 16571 536696 32.38766519823788 23.439996024084436 chrX 155270560 128068175 0.8248065505785515 1.8212131961636315 chrY 59373566 3253278 0.05479337387281067 1.7264184971527325