BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083779.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,422,102 number of mapped reads = 1,428,599 (58.98%) number of supplementary alignments = 9,563 (0.39%) number of secondary alignments = 0 number of mapped bases = 89,614,623 bp number of sequenced bases = 89,585,228 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 45,883 duplication rate = 2.71% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7148 >>>>>>> ACTG content number of A's = 25,430,852 bp (28.39%) number of C's = 16,995,090 bp (18.97%) number of T's = 27,356,047 bp (30.54%) number of G's = 19,802,168 bp (22.1%) number of N's = 1,071 bp (0%) GC percentage = 41.08% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 734,441 number of insertions = 6,426 mapped reads with insertion percentage = 0.45% number of deletions = 18,386 mapped reads with deletion percentage = 1.28% homopolymer indels = 46.3% >>>>>>> Coverage mean coverageData = 0.0289X std coverageData = 0.2293X There is a 2.61% of reference with a coverageData >= 1X There is a 0.22% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% 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 7098365 0.028478825735804285 0.3114165928136762 chr2 243199373 7898738 0.032478447220338845 0.28064731905860024 chr3 198022430 6013225 0.030366383242544797 0.1894420009166245 chr4 191154276 5882696 0.030774598000622284 0.19341990182692037 chr5 180915260 5579694 0.03084147793834528 0.19053513087875174 chr6 171115067 5297401 0.030958121297407434 0.2176300545543739 chr7 159138663 4973805 0.03125453554929012 0.27171309509576363 chr8 146364022 4636786 0.03167982087838499 0.24344077194021715 chr9 141213431 3869271 0.027400162807459865 0.2218231211180276 chr10 135534747 4115228 0.030362900223659988 0.24419739077000022 chr11 135006516 4211297 0.03119328699660689 0.21451960315592364 chr12 133851895 4133917 0.030884262042012927 0.19209091898401218 chr13 115169878 2867364 0.024896822413930143 0.17137977321120307 chr14 107349540 2657002 0.024750939780459235 0.1753939074795659 chr15 102531392 2590229 0.0252627897610129 0.17405538343286345 chr16 90354753 2386545 0.02641305433041248 0.18639353086675048 chr17 81195210 2186751 0.026932019758308404 0.18734525909188254 chr18 78077248 2512473 0.03217932322614649 0.38812729824149267 chr19 59128983 1358622 0.022977259730646814 0.25055802545673 chr20 63025520 1815356 0.028803506896888754 0.18785505866940463 chr21 48129895 1184094 0.0246020482695838 0.1764231480533313 chr22 51304566 913591 0.01780720647748974 0.14422088241917516 chrMT 16571 67468 4.071450123710096 2.9112967515626034 chrX 155270560 5163272 0.03325338686226159 0.21133723759924702 chrY 59373566 201433 0.0033926377270315886 0.07972052447079493