BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085109.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 = 1,171,129 number of mapped reads = 943,025 (80.52%) number of supplementary alignments = 8,238 (0.7%) number of secondary alignments = 0 number of mapped bases = 61,509,555 bp number of sequenced bases = 61,487,803 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 18,006 duplication rate = 1.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6042 >>>>>>> ACTG content number of A's = 18,587,287 bp (30.23%) number of C's = 11,572,129 bp (18.82%) number of T's = 18,337,727 bp (29.82%) number of G's = 12,989,384 bp (21.13%) number of N's = 1,276 bp (0%) GC percentage = 39.95% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 585,869 number of insertions = 4,845 mapped reads with insertion percentage = 0.51% number of deletions = 13,371 mapped reads with deletion percentage = 1.4% homopolymer indels = 45.86% >>>>>>> Coverage mean coverageData = 0.0199X std coverageData = 0.2007X There is a 1.85% of reference with a coverageData >= 1X There is a 0.1% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 4360427 0.017494146985495375 0.33158251260354477 chr2 243199373 6062284 0.02492721887074931 0.2061630420778572 chr3 198022430 4173761 0.021077213323763375 0.15307560209777793 chr4 191154276 3230659 0.0169007937860621 0.138586155022187 chr5 180915260 3463483 0.019144228076724983 0.1449151724876181 chr6 171115067 3838028 0.02242951522205815 0.1741755441037658 chr7 159138663 6004811 0.03773320000809608 0.23498478116674584 chr8 146364022 3925320 0.026818885859805082 0.35758320972748725 chr9 141213431 2519367 0.017840845464621564 0.16783756434301 chr10 135534747 4278318 0.031566207889110534 0.25481584845000094 chr11 135006516 2610283 0.019334496417935856 0.1803083817709443 chr12 133851895 2795321 0.020883686405784543 0.15296845109301063 chr13 115169878 1067774 0.009271295746271434 0.10006718677621387 chr14 107349540 2070136 0.019284069591728105 0.14807922690020475 chr15 102531392 938666 0.009154913258175603 0.09952388608795527 chr16 90354753 1607457 0.017790508486033932 0.14500402930199158 chr17 81195210 783706 0.00965212110418829 0.10965756018673221 chr18 78077248 1585051 0.020301061328391084 0.26401123858670505 chr19 59128983 1050017 0.01775807644112533 0.2142341803867304 chr20 63025520 1184690 0.01879698890227324 0.14374919447571524 chr21 48129895 838589 0.01742345375987211 0.14139702453720682 chr22 51304566 441352 0.008602587145947204 0.09598382587756626 chrMT 16571 8854 0.5343069217307345 0.7611098071079043 chrX 155270560 2548367 0.01641242873085535 0.14189254952755906 chrY 59373566 122834 0.0020688331234812473 0.05936526512327867