Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.

ALE, Flask, Isolate	Predicted Mutations	Mean Coverage	Total Reads	Percent Mapped	Mapped Reads	Average Read Length
A1 F4 I96 R1	227	23.3	882352	98.0%	864704	126.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	716,126	A→G	intergenic (‑210/+48)	speF ← / ← BW25113_RS26090	ornithine decarboxylase SpeF/leader peptide SpeFL

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	716,126	0	A	G	100.0%	93.6 / NA	25	intergenic (‑210/+48)	speF/BW25113_RS26090	ornithine decarboxylase SpeF/leader peptide SpeFL
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (12/13); total (12/13)

GCAAAGTTACCCCGCTGATAAATAAATCAGGTAGATTGCTTTTTTCAGAATGCAGAAACCCTTACCAGTCAGGTGGCTGATAATACAAGGGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATACAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTGAAGAAGTGAAAGTCGAAGCTATTGCGATGAGCAAACTTCATAATATGAGTTGTCCGCCTTATATGGGGCATAGT  >  NZ_CP009273/715990‑716260

gCAAAGTTACCCCGCTGATAAATAAATCAGGTAGATTGCTTTTTTCAGAATGCAGAAACCCTTACCAGTCAGGTGGCTGATAATACAAGGGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCa                                                                                                                                      <  1:225865/139‑1 (MQ=255)

gCAAAGTTACCCCGCTGATAAATAAATCAGGTAGATTGCTTTTTTCAGAATGCAGAAACCCTTACCAGTCAGGTGGCTGATAATACAAGGGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCa                                                                                                                                      <  1:317485/139‑1 (MQ=255)

     gTTACCCCGCTGATAAATAAATCAGGTAGATTGCTTTTTTCAGAATGCAGAAACCCTTACCAGTCAGGTGGCTGATAATACAAGGGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCagagag                                                                                                                                 <  2:241196/139‑1 (MQ=255)

              cTGATAAATAAATCAGGTAGATTGCTTTTTTCAGAATGCAGAAACCCTTACCAGTCAGGTGGCTGATAATACAAGGGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGa                                                                                                                        >  1:375399/1‑139 (MQ=255)

              cTGATAAATAAATCAGGTAGATTGCTTTTTTCAGAATGCAGAAACCCTTACCAGTCAGGTGGCTGATAATACAAGGGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGa                                                                                                                        >  1:324718/1‑139 (MQ=255)

                         atCAGGTAGATTGCTTTTTTCAGAATGCAGAAACCCTTACCAGTCAGGTGGCTGATAATACAAGGGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCt                                                                                                              >  1:273832/1‑138 (MQ=255)

                            aGGTAGATTGCTTTTTTCAGAATGCAGAAACCCTTACCAGTCAGGTGGCTGATAATACAAGGGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGaa                                                                                                           <  1:231503/138‑1 (MQ=255)

                                  aTTGCTTTTTTCAGAATGCAGAAACCCTTACCAGTCAGGTGGCTGATAATACAAGGGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCt                                                                                                    >  2:438363/1‑139 (MQ=255)

                                           ttCAGAATGCAGAAACCCTTACCAGTCAGGTGGCTGATAATACAAGGGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGt                                                                                            <  2:273832/138‑1 (MQ=255)

                                                    cAGAAACCCTTACCAGTCAGGTGGCTGATAATACAAGGGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACg                                                                                   <  1:326803/138‑1 (MQ=255)

                                                              tACCAGTCAGGTGGCTGATAATACAAGGGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTgaag                                                                         >  1:224467/1‑138 (MQ=255)

                                                                     cAGGTGGCTGATAATACAAGGGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTgaa                                                                          <  2:132181/130‑1 (MQ=255)

                                                                     cAGGTGGCTGATAATACAAGGGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTgaa                                                                          >  1:132181/1‑130 (MQ=255)

                                                                                           ttAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGt                                                                                                <  1:14875/86‑1 (MQ=255)

                                                                                           ttAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGt                                                                                                >  2:14875/1‑86 (MQ=255)

                                                                                                     aTGAGCACTGCGGAATACAGGCATATGCCTGT‑ATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTGAAGAAGTGAAAGTCGAAGCTATTGCGATGAGCAAACTTCataat                                <  1:257115/139‑1 (MQ=255)

                                                                                                               cGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTGAAGAAGTGAAAGTCGAAGCTATTGCGATGAGCAAACTTCATAATATGAGTTGt                       <  1:231166/139‑1 (MQ=255)

                                                                                                                  aaTACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTGAAGAAGTGAAAGTCGAAGCTATTGCGATGAGCAAACTTCATAATATGAGTTGTCCg                    <  2:162017/139‑1 (MQ=255)

                                                                                                                    tACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTGAAGAAGTGAAAGTCGAAGCTATTGCGATGAGCAAACTTCATAATATGAGTTGTCCGcc                  <  2:224467/139‑1 (MQ=255)

                                                                                                                         gCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTGAAGAAGTGAAAGTCGAAGCTATTGCGATGAGCAAACTTCATAATATGAGTTGTCCGCCTtata             >  2:274956/1‑139 (MQ=255)

                                                                                                                            tatGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTGAAGAAGTGAAAGTCGAAGCTATTGCGATGAGCAAACTTCATAATATGAGTTGTCCGCCTTATATgg          >  2:326209/1‑139 (MQ=255)

                                                                                                                                   gTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTGAAGAAGTGAAAGTCGAAGCTATTGCGATGAGCAAACTTCATAATATGAGTTGTCCGcc                  <  2:117487/124‑1 (MQ=255)

                                                                                                                                   gTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGGGCCCTTAGTCGGTAGACTAACGGGCATTGAAGAAGTGAAAGTCGAAGCTATTGCGATGAGCAAACTTCATAATATGAGTTGTCCGcc                  >  1:117487/1‑124 (MQ=255)

                                                                                                                                    tAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTGAAGAAGTGAAAGTCGAAGCTATTGCGATGAGCAAACTTCATAATATGAGTTGTCCGCCTTATATGGGGCATAGt  >  2:293450/1‑139 (MQ=255)

                                                                                                                                    tAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTGAAGAAGTGAAAGTCGAAGCTATTGCGATGAGCAAACTTCATAATATGAGTTGTCCGCCTTATATGGGGCATAGt  >  2:40364/1‑139 (MQ=255)

GCAAAGTTACCCCGCTGATAAATAAATCAGGTAGATTGCTTTTTTCAGAATGCAGAAACCCTTACCAGTCAGGTGGCTGATAATACAAGGGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATACAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTGAAGAAGTGAAAGTCGAAGCTATTGCGATGAGCAAACTTCATAATATGAGTTGTCCGCCTTATATGGGGCATAGT  >  NZ_CP009273/715990‑716260

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

BRESEQ :: bam2aln output

AGCAAAGTTACCCCGCTGATAAATAAATCAGGTAGATTGCTTTTTTCAGAATGCAGAAACCCTTACCAGTCAGGTGGCTGATAATACAAGGGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATACAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTGAAGAAGTGAAAGTCGAAGCTATTGCGATGAGCAAACTTCATAATATGAGTTGTCCGCCTTATATGGGGCATAGTGCGGCTGTTATTTTC  >  NZ_CP009273/715989‑716275

AGCAAAGTTACCCCGCTGATAAATAAATCAGGTAGATTGCTTTTTTCAGAATGCAGAAACCCTTACCAGTCAGGTGGCTGATAATACAAGGGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGA                                                                                                                                          <  SRR3722119.228259/151‑1 (MQ=60)

AGCAAAGTTACCCCGCTGATAAATAAATCAGGTAGATTGCTTTTTTCAGAATGCAGAAACCCTTACCAGTCAGGTGGCTGATAATACAAGGGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGA                                                                                                                                          <  SRR3722119.320731/151‑1 (MQ=60)

    AAGTTACCCCGCTGATAAATAAATCAGGTAGATTGCTTTTTTCAGAATGCAGAAACCCTTACCAGTCAGGTGGCTGATAATACAAGGGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGAC                                                                                                                                      >  SRR3722119.328032/1‑151 (MQ=60)

    AAGTTACCCCGCTGATAAATAAATCAGGTAGATTGCTTTTTTCAGAATGCAGAAACCCTTACCAGTCAGGTGGCTGATAATACAAGGGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGAC                                                                                                                                      >  SRR3722119.379183/1‑151 (MQ=60)

               CTGATAAATAAATCAGGTAGATTGCTTTTTTCAGAATGCAGAAACCCTTACCAGTCAGGTGGCTGATAATACAAGGGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTG                                                                                                                            >  SRR3722119.276675/1‑150 (MQ=60)

                            CAGGTAGATTGCTTTTTTCAGAATGCAGAAACCCTTACCAGTCAGGTGGCTGATAATACAAGGGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGT                                                                                                               <  SRR3722119.233939/150‑1 (MQ=60)

                                       tcgccttagtctcgtgggctcggagatgtgtataagagacagTAATACAAGGGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAA                                                                                                    <  SRR3722119.15001/108‑1 (MQ=60)

                                                    GCAGAAACCCTTACCAGTCAGGTGGCTGATAATACAAGGGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTGAAGA                                                                                       >  SRR3722119.226855/1‑150 (MQ=60)

                                                    GCAGAAACCCTTACCAGTCAGGTGGCTGATAATACAAGGGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTGAAGA                                                                                       <  SRR3722119.330133/150‑1 (MQ=60)

                                                           CCCTTACCAGTCAGGTGGCTGATAATACAAGGGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTGAAGAAGTGAA                                                                                 >  SRR3722119.133529/1‑149 (MQ=60)

                                                                                                     AATGAGCACTGCGGAATACAGGCATATGCCTGT‑ATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTGAAGAAGTGAAAGTCGAAGCTATTGCGATGAGCAAACTTCATAATATGAGTTGTCC                                    <  SRR3722119.259786/151‑1 (MQ=60)

                                                                                                               GCGGAATACAGGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTGAAGAAGTGAAAGTCGAAGCTATTGCGATGAGCAAACTTCATAATATGAGTTGTCCGCCTTATAT                           <  SRR3722119.233597/151‑1 (MQ=60)

                                                                                                                         GGCATATGCCTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGGGCCCTTAGTCGGTAGACTAACGGGCATTGAAGAAGTGAAAGTCGAAGCTATTGCGATGAGCAAACTTCATAATATGAGTTGTCCGCCTTATATGGGGCctgtc                 >  SRR3722119.118640/1‑146 (MQ=60)

                                                                                                                                  CTGTAATGCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTGAAGAAGTGAAAGTCGAAGCTATTGCGATGAGCAAACTTCATAATATGAGctgtctcttatacacatctccgagcccacgagac        >  SRR3722119.163586/1‑117 (MQ=60)

                                                                                                                                         GCAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTGAAGAAGTGAAAGTCGAAGCTATTGCGATGAGCAAACTTCATAATATGAGTTGTCCGCCTTATATGGGGCATAGTGCGGCTGTTATTTTC  <  SRR3722119.442747/150‑1 (MQ=60)

AGCAAAGTTACCCCGCTGATAAATAAATCAGGTAGATTGCTTTTTTCAGAATGCAGAAACCCTTACCAGTCAGGTGGCTGATAATACAAGGGTTAACAGAGAATGAGCACTGCGGAATACAGGCATATGCCTGTAATACAGAGAGTCAGGAAGACCTGTACGCTGAAGTGCCCTTAGTCGGTAGACTAACGGGCATTGAAGAAGTGAAAGTCGAAGCTATTGCGATGAGCAAACTTCATAATATGAGTTGTCCGCCTTATATGGGGCATAGTGCGGCTGTTATTTTC  >  NZ_CP009273/715989‑716275

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`