BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006447.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 1,221,121 number of mapped reads = 1,162,449 (95.2%) number of supplementary alignments = 3,243 (0.27%) number of secondary alignments = 0 number of mapped bases = 65,055,911 bp number of sequenced bases = 65,036,970 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,873 duplication rate = 1.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2214 >>>>>>> ACTG content number of A's = 18,432,094 bp (28.34%) number of C's = 13,764,778 bp (21.16%) number of T's = 18,480,520 bp (28.42%) number of G's = 14,357,676 bp (22.08%) number of N's = 1,902 bp (0%) GC percentage = 43.24% >>>>>>> Mismatches and indels general error rate = 0.0043 number of mismatches = 270,782 number of insertions = 4,264 mapped reads with insertion percentage = 0.37% number of deletions = 11,377 mapped reads with deletion percentage = 0.97% homopolymer indels = 45.95% >>>>>>> Coverage mean coverageData = 0.021X std coverageData = 0.1793X There is a 1.94% of reference with a coverageData >= 1X There is a 0.13% 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 5351248 0.021469346710273594 0.2158595035693596 chr2 243199373 5319410 0.021872630403533155 0.17865525447227784 chr3 198022430 4397177 0.0222054491503816 0.157744397649036 chr4 191154276 4236916 0.022164903075461415 0.16417021722996342 chr5 180915260 3895780 0.021533728000612 0.15514691048944854 chr6 171115067 3653784 0.021352789465348482 0.15939006584303086 chr7 159138663 3602564 0.022637892841917365 0.1914334849062244 chr8 146364022 3325387 0.022719975541530282 0.3081199127429095 chr9 141213431 2824449 0.020001277357250814 0.16232586991238715 chr10 135534747 2968092 0.021899122296660942 0.1839845705013409 chr11 135006516 3086948 0.02286517785556365 0.1676144596558402 chr12 133851895 3062937 0.022883030531618546 0.16121779576482062 chr13 115169878 2052431 0.017820901051922623 0.14101116033762398 chr14 107349540 2010013 0.018724001984545068 0.14772581415013372 chr15 102531392 1987132 0.019380718053647415 0.1477101712767399 chr16 90354753 1854214 0.020521488227630925 0.1679001227507434 chr17 81195210 1991948 0.024532826505405923 0.1733241819427671 chr18 78077248 1714764 0.02196240318306301 0.21028442863398863 chr19 59128983 1503390 0.025425602195796263 0.2101121187559497 chr20 63025520 1496981 0.023751981736921807 0.16506449538416718 chr21 48129895 1235616 0.02567252639965244 0.18167695096938216 chr22 51304566 901392 0.017569430369998647 0.1470582711425562 chrMT 16571 31741 1.9154547100356043 1.781219750543782 chrX 155270560 1962524 0.012639382507540386 0.12187572443492282 chrY 59373566 589073 0.00992146909282828 0.14697649573043844