BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174031.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 12,461,048 number of mapped reads = 12,136,362 (97.39%) number of supplementary alignments = 1,227,530 (9.85%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,068,291 number of mapped paired reads (second in pair) = 6,068,071 number of mapped paired reads (both in pair) = 11,915,700 number of mapped paired reads (singletons) = 220,662 number of mapped bases = 1,437,277,540 bp number of sequenced bases = 1,436,460,239 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,369,606 duplication rate = 65.2% >>>>>>> Insert size mean insert size = 777,241.2778 std insert size = 8,101,401.5009 median insert size = 207 >>>>>>> Mapping quality mean mapping quality = 52.7351 >>>>>>> ACTG content number of A's = 428,485,486 bp (29.83%) number of C's = 284,771,356 bp (19.82%) number of T's = 427,606,331 bp (29.77%) number of G's = 295,579,073 bp (20.58%) number of N's = 17,993 bp (0%) GC percentage = 40.4% >>>>>>> Mismatches and indels general error rate = 0.0107 number of mismatches = 15,016,640 number of insertions = 149,184 mapped reads with insertion percentage = 1.19% number of deletions = 334,723 mapped reads with deletion percentage = 2.69% homopolymer indels = 42.82% >>>>>>> Coverage mean coverageData = 0.4643X std coverageData = 6.2889X There is a 9.48% of reference with a coverageData >= 1X There is a 7.59% of reference with a coverageData >= 2X There is a 5.91% of reference with a coverageData >= 3X There is a 4.84% of reference with a coverageData >= 4X There is a 3.68% of reference with a coverageData >= 5X There is a 2.96% of reference with a coverageData >= 6X There is a 2.2% of reference with a coverageData >= 7X There is a 1.78% of reference with a coverageData >= 8X There is a 1.33% of reference with a coverageData >= 9X There is a 1.1% of reference with a coverageData >= 10X There is a 0.82% of reference with a coverageData >= 11X There is a 0.7% of reference with a coverageData >= 12X There is a 0.52% of reference with a coverageData >= 13X There is a 0.45% of reference with a coverageData >= 14X There is a 0.34% of reference with a coverageData >= 15X There is a 0.3% of reference with a coverageData >= 16X There is a 0.23% of reference with a coverageData >= 17X There is a 0.2% of reference with a coverageData >= 18X There is a 0.16% of reference with a coverageData >= 19X There is a 0.14% of reference with a coverageData >= 20X There is a 0.11% of reference with a coverageData >= 21X There is a 0.1% of reference with a coverageData >= 22X There is a 0.08% of reference with a coverageData >= 23X There is a 0.07% of reference with a coverageData >= 24X There is a 0.06% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% 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 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% 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 110368334 0.4428006379972068 4.496956933596084 chr2 243199373 116832986 0.4804000296497475 19.711689411979677 chr3 198022430 122882080 0.6205462684201987 2.3111319167257265 chr4 191154276 67942422 0.35543239430333223 2.4109138909414227 chr5 180915260 90975743 0.5028638435475261 1.997774756716757 chr6 171115067 80708072 0.4716596464296157 2.680950976978188 chr7 159138663 77886056 0.48942258613797707 3.7574738044481246 chr8 146364022 81781381 0.5587533048251434 3.2952575203556345 chr9 141213431 61536361 0.43576847162647014 2.934921741018569 chr10 135534747 65923298 0.4863940757568242 5.859652033607629 chr11 135006516 51772892 0.38348439419027747 1.8565322415754253 chr12 133851895 66073963 0.493634871586988 2.0223883827152074 chr13 115169878 31538372 0.27384219335545357 1.4763877483167962 chr14 107349540 45559071 0.42439931274973325 1.8762922460619516 chr15 102531392 49342240 0.48124032101310005 1.9938278991494605 chr16 90354753 46149167 0.5107552781423684 3.105068664661728 chr17 81195210 64520939 0.7946397207421473 3.219789123069033 chr18 78077248 26524316 0.33971888968217734 5.074252135056834 chr19 59128983 24354062 0.41188027874587324 3.194089674952346 chr20 63025520 67560519 1.0719549636401255 3.8068998316820832 chr21 48129895 18599608 0.38644605395461595 2.023764910623515 chr22 51304566 12455013 0.24276617016894753 1.3785299610946042 chrMT 16571 3005717 181.3841651077183 142.6985263646132 chrX 155270560 50415986 0.324697650346595 1.630240112945958 chrY 59373566 2568942 0.0432674365558572 1.4998271649309725