BamQC report ----------------------------------- >>>>>>> Input bam file = SRR630575.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 37,205,002 number of mapped reads = 36,431,621 (97.92%) number of supplementary alignments = 61,254 (0.16%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 18,289,131 number of mapped paired reads (second in pair) = 18,142,490 number of mapped paired reads (both in pair) = 36,213,594 number of mapped paired reads (singletons) = 218,027 number of mapped bases = 3,565,138,341 bp number of sequenced bases = 3,562,435,039 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,122,750 duplication rate = 11.77% >>>>>>> Insert size mean insert size = 27,024.0373 std insert size = 1,639,478.5454 median insert size = 205 >>>>>>> Mapping quality mean mapping quality = 54.1731 >>>>>>> ACTG content number of A's = 1,029,617,919 bp (28.9%) number of C's = 727,984,945 bp (20.44%) number of T's = 1,036,860,792 bp (29.11%) number of G's = 767,434,204 bp (21.54%) number of N's = 537,179 bp (0.02%) GC percentage = 41.98% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 31,504,658 number of insertions = 672,937 mapped reads with insertion percentage = 1.81% number of deletions = 2,002,739 mapped reads with deletion percentage = 5.34% homopolymer indels = 54.64% >>>>>>> Coverage mean coverageData = 1.1516X std coverageData = 5.5811X There is a 16.95% of reference with a coverageData >= 1X There is a 12.1% of reference with a coverageData >= 2X There is a 9.31% of reference with a coverageData >= 3X There is a 7.57% of reference with a coverageData >= 4X There is a 6.34% of reference with a coverageData >= 5X There is a 5.42% of reference with a coverageData >= 6X There is a 4.7% of reference with a coverageData >= 7X There is a 4.12% of reference with a coverageData >= 8X There is a 3.65% of reference with a coverageData >= 9X There is a 3.26% of reference with a coverageData >= 10X There is a 2.93% of reference with a coverageData >= 11X There is a 2.64% of reference with a coverageData >= 12X There is a 2.39% of reference with a coverageData >= 13X There is a 2.18% of reference with a coverageData >= 14X There is a 1.99% of reference with a coverageData >= 15X There is a 1.82% of reference with a coverageData >= 16X There is a 1.67% of reference with a coverageData >= 17X There is a 1.54% of reference with a coverageData >= 18X There is a 1.42% of reference with a coverageData >= 19X There is a 1.31% of reference with a coverageData >= 20X There is a 1.22% of reference with a coverageData >= 21X There is a 1.13% of reference with a coverageData >= 22X There is a 1.05% of reference with a coverageData >= 23X There is a 0.97% of reference with a coverageData >= 24X There is a 0.91% of reference with a coverageData >= 25X There is a 0.85% of reference with a coverageData >= 26X There is a 0.79% of reference with a coverageData >= 27X There is a 0.74% of reference with a coverageData >= 28X There is a 0.69% of reference with a coverageData >= 29X There is a 0.65% of reference with a coverageData >= 30X There is a 0.61% of reference with a coverageData >= 31X There is a 0.58% of reference with a coverageData >= 32X There is a 0.54% of reference with a coverageData >= 33X There is a 0.51% of reference with a coverageData >= 34X There is a 0.48% of reference with a coverageData >= 35X There is a 0.45% of reference with a coverageData >= 36X There is a 0.43% of reference with a coverageData >= 37X There is a 0.4% of reference with a coverageData >= 38X There is a 0.38% of reference with a coverageData >= 39X There is a 0.36% of reference with a coverageData >= 40X There is a 0.34% of reference with a coverageData >= 41X There is a 0.32% of reference with a coverageData >= 42X There is a 0.31% of reference with a coverageData >= 43X There is a 0.29% of reference with a coverageData >= 44X There is a 0.28% of reference with a coverageData >= 45X There is a 0.26% of reference with a coverageData >= 46X There is a 0.25% of reference with a coverageData >= 47X There is a 0.24% of reference with a coverageData >= 48X There is a 0.22% of reference with a coverageData >= 49X There is a 0.21% of reference with a coverageData >= 50X There is a 0.2% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 301031124 1.207744730152548 6.279747536812176 chr2 243199373 295154253 1.2136308139248368 6.2147347601122656 chr3 198022430 241998232 1.2220748528335905 5.282987707839255 chr4 191154276 201233952 1.052730580821535 5.036151447113714 chr5 180915260 210328390 1.1625795966575734 5.052881531693463 chr6 171115067 199942668 1.168469098048508 5.150375863074962 chr7 159138663 184033128 1.156432538332938 5.190877707380947 chr8 146364022 175650397 1.200092718140801 5.206035625828508 chr9 141213431 157469706 1.115118476230494 6.216022353912165 chr10 135534747 173720179 1.2817390583980652 5.541227035458481 chr11 135006516 171801867 1.2725450007168544 5.799200904120322 chr12 133851895 161023297 1.2029960203402426 5.375330720504674 chr13 115169878 102030520 0.8859132420023923 4.347888850344733 chr14 107349540 108759702 1.0131361717991525 4.757641650559273 chr15 102531392 113792329 1.1098291633454074 5.089459111915658 chr16 90354753 114639994 1.268776574487454 7.662705259843359 chr17 81195210 103718452 1.2773961912285219 5.872648991274588 chr18 78077248 93155466 1.1931192298171165 5.806155433985921 chr19 59128983 64010335 1.082554303360841 5.802424271127655 chr20 63025520 90359257 1.4336931611194956 6.2417578699600025 chr21 48129895 45685404 0.949210547831031 6.69308910548973 chr22 51304566 50607517 0.9864135094720419 5.531947572711661 chrMT 16571 7192 0.434011224428218 2.009637141625308 chrX 155270560 199928147 1.2876114248573587 5.513270881161692 chrY 59373566 5056833 0.08516977066865077 2.587592449658008