BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3212677.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 = 2,978,966 number of mapped reads = 2,798,630 (93.95%) number of supplementary alignments = 13,544 (0.45%) number of secondary alignments = 0 number of mapped bases = 191,105,233 bp number of sequenced bases = 191,041,259 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 158,498 duplication rate = 4.75% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.1047 >>>>>>> ACTG content number of A's = 54,647,873 bp (28.61%) number of C's = 36,283,763 bp (18.99%) number of T's = 59,731,492 bp (31.27%) number of G's = 40,375,976 bp (21.13%) number of N's = 2,155 bp (0%) GC percentage = 40.13% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 1,490,758 number of insertions = 12,953 mapped reads with insertion percentage = 0.46% number of deletions = 36,118 mapped reads with deletion percentage = 1.28% homopolymer indels = 48.3% >>>>>>> Coverage mean coverageData = 0.0617X std coverageData = 0.4237X There is a 4.41% of reference with a coverageData >= 1X There is a 1.15% of reference with a coverageData >= 2X There is a 0.35% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 14965893 0.06004355351235013 0.5444713334282807 chr2 243199373 16392417 0.06740320420151741 0.4686322988232632 chr3 198022430 12877650 0.06503126943750766 0.33939512262950167 chr4 191154276 12880054 0.06738041266730543 0.36133258275441216 chr5 180915260 11891484 0.06572957969383014 0.34278273872826515 chr6 171115067 11305028 0.06606681806693271 0.45810045886850903 chr7 159138663 10416251 0.06545393057625475 0.5570832813245079 chr8 146364022 9477578 0.0647534678980057 0.48662962378373675 chr9 141213431 7406478 0.05244882124562217 0.4067069159981863 chr10 135534747 8955685 0.06607667183677998 0.4027700749964964 chr11 135006516 8965145 0.06640527632014442 0.4516973982361129 chr12 133851895 9265292 0.06922047685615508 0.3543095733403826 chr13 115169878 5957107 0.05172452296945213 0.3024147474363885 chr14 107349540 6078202 0.05662066181187176 0.3360015202695688 chr15 102531392 5546019 0.05409093636415275 0.31488095014693784 chr16 90354753 5358399 0.05930400805810404 0.3460628165901852 chr17 81195210 5236142 0.06448831156419202 0.37196933999206505 chr18 78077248 5166607 0.06617301624155605 0.7222644035805396 chr19 59128983 3298742 0.0557889182704191 0.43217679746860416 chr20 63025520 3952252 0.06270875670680702 0.3433729244540663 chr21 48129895 2292138 0.047623997517551205 0.3155344032514105 chr22 51304566 2225716 0.04338241551443979 0.273220115674714 chrMT 16571 200984 12.128658499788788 9.059447030756035 chrX 155270560 10563413 0.06803229794495493 0.37332485571665686 chrY 59373566 430557 0.0072516614548636 0.15608854960721458