BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975209.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP029757/SRP029757.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 = 7,066,336 number of mapped reads = 6,993,094 (98.96%) number of supplementary alignments = 99,743 (1.41%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,501,450 number of mapped paired reads (second in pair) = 3,491,644 number of mapped paired reads (both in pair) = 6,966,808 number of mapped paired reads (singletons) = 26,286 number of mapped bases = 958,763,303 bp number of sequenced bases = 958,042,038 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,532,010 duplication rate = 17.66% >>>>>>> Insert size mean insert size = 79,683.6095 std insert size = 2,681,202.2531 median insert size = 177 >>>>>>> Mapping quality mean mapping quality = 53.3919 >>>>>>> ACTG content number of A's = 285,289,923 bp (29.78%) number of C's = 189,239,812 bp (19.75%) number of T's = 287,705,541 bp (30.03%) number of G's = 195,704,048 bp (20.43%) number of N's = 102,714 bp (0.01%) GC percentage = 40.18% >>>>>>> Mismatches and indels general error rate = 0.0127 number of mismatches = 11,586,132 number of insertions = 205,010 mapped reads with insertion percentage = 2.78% number of deletions = 348,471 mapped reads with deletion percentage = 4.79% homopolymer indels = 45.42% >>>>>>> Coverage mean coverageData = 0.3097X std coverageData = 5.504X There is a 13.02% of reference with a coverageData >= 1X There is a 8.36% of reference with a coverageData >= 2X There is a 3.19% of reference with a coverageData >= 3X There is a 1.92% of reference with a coverageData >= 4X There is a 0.88% of reference with a coverageData >= 5X There is a 0.52% of reference with a coverageData >= 6X There is a 0.27% of reference with a coverageData >= 7X There is a 0.17% of reference with a coverageData >= 8X There is a 0.1% of reference with a coverageData >= 9X There is a 0.07% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% 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 0.01% 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 0.01% 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 73478783 0.2947987961081148 5.494621786565779 chr2 243199373 87125977 0.3582491843019677 5.7755476615349135 chr3 198022430 66776062 0.337214637755935 1.1539323151986312 chr4 191154276 69984775 0.36611671192749046 3.962382721281744 chr5 180915260 59575059 0.329298142124661 1.0354886626834992 chr6 171115067 57662578 0.3369813015939736 2.7148797519720755 chr7 159138663 52215993 0.32811632330981694 5.28344837447568 chr8 146364022 49785566 0.34014893359517 1.7883663486876389 chr9 141213431 42689105 0.3023020168669367 9.468314797577369 chr10 135534747 56439528 0.4164210967981517 14.7078917482679 chr11 135006516 45842745 0.33955949948371383 4.1731556377753 chr12 133851895 38961991 0.29108284944340906 0.9594517906292918 chr13 115169878 31044796 0.2695565588773134 0.8810437460575476 chr14 107349540 28896213 0.26917873145986465 1.0122054245506074 chr15 102531392 24954364 0.24338267054835264 0.846100202902031 chr16 90354753 37448305 0.414458606289367 10.216140590438878 chr17 81195210 21228746 0.2614531817825214 5.178050996152614 chr18 78077248 28881570 0.3699101945806287 9.459864162135055 chr19 59128983 10368508 0.17535407297636085 3.0287186081323014 chr20 63025520 18097941 0.2871525851750212 1.5567689946728283 chr21 48129895 12186276 0.2531955658743905 2.2946565338125136 chr22 51304566 7216207 0.14065428406508693 0.6704811596160795 chrMT 16571 65435 3.948765916359906 3.2519174977379945 chrX 155270560 33027654 0.21271034251438264 1.539985335844846 chrY 59373566 4809126 0.08099776253964601 8.041333874836878