BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038419.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 14,942,040 number of mapped reads = 14,212,577 (95.12%) number of supplementary alignments = 275,326 (1.84%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,192,955 number of mapped paired reads (second in pair) = 7,019,622 number of mapped paired reads (both in pair) = 14,014,078 number of mapped paired reads (singletons) = 198,499 number of mapped bases = 2,039,881,465 bp number of sequenced bases = 2,038,374,071 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,517,308 duplication rate = 10.13% >>>>>>> Insert size mean insert size = 79,011.7008 std insert size = 2,636,643.5285 median insert size = 243 >>>>>>> Mapping quality mean mapping quality = 53.6589 >>>>>>> ACTG content number of A's = 602,535,900 bp (29.56%) number of C's = 413,142,290 bp (20.27%) number of T's = 600,979,359 bp (29.48%) number of G's = 421,674,212 bp (20.69%) number of N's = 42,310 bp (0%) GC percentage = 40.96% >>>>>>> Mismatches and indels general error rate = 0.0157 number of mismatches = 30,914,408 number of insertions = 391,998 mapped reads with insertion percentage = 2.58% number of deletions = 720,849 mapped reads with deletion percentage = 4.87% homopolymer indels = 46.25% >>>>>>> Coverage mean coverageData = 0.6589X std coverageData = 12.4062X There is a 27.59% of reference with a coverageData >= 1X There is a 14.78% of reference with a coverageData >= 2X There is a 7.32% of reference with a coverageData >= 3X There is a 4.18% of reference with a coverageData >= 4X There is a 2.28% of reference with a coverageData >= 5X There is a 1.33% of reference with a coverageData >= 6X There is a 0.78% of reference with a coverageData >= 7X There is a 0.48% of reference with a coverageData >= 8X There is a 0.3% of reference with a coverageData >= 9X There is a 0.2% of reference with a coverageData >= 10X There is a 0.14% of reference with a coverageData >= 11X There is a 0.1% of reference with a coverageData >= 12X There is a 0.08% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% 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 121029916 0.48557518338138866 16.67584897145845 chr2 243199373 223976725 0.9209593028021499 16.66470577501145 chr3 198022430 150537456 0.760204063751768 1.58478002067321 chr4 191154276 121195182 0.6340176350541068 11.70442071664244 chr5 180915260 113913643 0.6296519320702963 1.5228281107299089 chr6 171115067 156783881 0.9162482518269417 17.52858182597544 chr7 159138663 108059246 0.6790257248799432 9.746964491392735 chr8 146364022 92620663 0.6328103159121987 3.413339784001332 chr9 141213431 74395534 0.5268304400875297 19.809460372072355 chr10 135534747 85516542 0.6309565915226152 25.218704870162224 chr11 135006516 111144875 0.8232556345650753 9.373446878325153 chr12 133851895 65774686 0.4913989899059703 1.2695785278191998 chr13 115169878 131151152 1.138762619857946 2.017030583614346 chr14 107349540 34747290 0.32368364130857014 1.3009685702222482 chr15 102531392 31950622 0.31161794818898003 0.8938414561351811 chr16 90354753 80503658 0.8909731400627038 16.869314191629826 chr17 81195210 49293033 0.6070928691483155 8.388701355208438 chr18 78077248 31566022 0.4042921953396718 17.91687050219789 chr19 59128983 22300538 0.37715071135250205 9.323476838857102 chr20 63025520 56117083 0.8903866719386052 3.7624727404101734 chr21 48129895 18270058 0.3795989581942782 5.4301003758244955 chr22 51304566 9726361 0.18958080651145162 0.7885683252618629 chrMT 16571 2101255 126.80315008146762 70.50890191371491 chrX 155270560 106052689 0.6830186546631892 2.6960271885107927 chrY 59373566 41153355 0.6931258769264423 19.731714246103746