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
A9 F28 I1 R1	120	56.0	1898522	99.4%	1887130	138.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,308,219	T→C	T236A (ACC→GCC)	nlpI ←	lipoprotein NlpI

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,308,219	0	T	C	100.0%	136.3 / NA	38	T236A (ACC→GCC)	nlpI	lipoprotein NlpI
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (23/15); total (23/15)

CAGGAGCGATAATTCCAACAATGCGTATCGGTGCTCAACAAAGTTATGAACGTTGTTGGCAACCGCCAGTTTGAACAGTGCCGTGGCGCTGTCCAAATCCCCCAGACTTAGGTAGTACTTACCTAAATAGAAGTTGGTTTCACTGAGATGCTCAGCGAGCGAGGTGTTATCCGTTGCGTCCGCCTTGAGCCTTTCCATTAACGTTTGTTCGCTAATGTTGCCCAGGTAGAACTCGACAATGTTCCATCCCCACTGTTCCTTATCCGATTT  >  NC_000913/3308082‑3308351

aaGGGGCGATAATTCCAACAATGGGTTTCGGTGCTCAACAAAGTTATGAAGGTTGTTGGCAACCGCCAGTTTGAACAGTGCCGTGGCGCTGTCCAAATCCCCCAGACTTAGGTAGTACTTACCTAAATAGAAGTTGGctt                                                                                                                                    <  2:449878/139‑1 (MQ=255)

                  caaTGCGTATCGGTGCTCAACAAAGTTATGAACGTTGTTGGCAACCGCCAGTTTGAACAGTGCCGTGGCGCTGTCCAAATCCCCCAGACTTAGGTAGTACTTACCTAAATAGAAGTTGGCTTCACTGAGATGCTCagcga                                                                                                                  >  1:791082/1‑140 (MQ=255)

                     tGCGTATCGGTGCTCAACAAAGTTATGAACGTTGTTGGCAACCGCCAGTTTGAACAGTGCCGTGGCGCTGTCCAAATCCCCCAGACTTAGGTAGTACTTACCTAAATAGAAGTTGGCTTCACTGAGATGCTCagcgagcg                                                                                                               <  1:264764/140‑1 (MQ=255)

                     tGCGTATCGGTGCTCAACAAAGTTATGAACGTTGTTGGCAACCGCCAGTTTGAACAGTGCCGTGGCGCTGTCCAAATCCCCCAGACTTAGGTAGTACTTACCTAAATAGAAGTTGGCTTCACTGAGATGCTCagcgagcg                                                                                                               <  2:342877/140‑1 (MQ=255)

                      gCGTATCGGTGCTCAACAAAGTTATGAACGTTGTTGGCAACCGCCAGTTTGAACAGTGCCGTGGCGCTGTCCAAATCCCCCAGACTTAGGTAGTACTTACCTAAATAGAAGTTGGCTTCACTGAGATGCTCAgcgagcga                                                                                                              <  1:178295/140‑1 (MQ=255)

                      gCGTATCGGTGCTCAACAAAGTTATGAACGTTGTTGGCAACCGCCAGTTTGAACAGTGCCGTGGCGCTGTCCAAATCCCCCAGACTTAGGTAGTACTTACCTAAATAGAAGTTGGCTTCACTGAGATGCTCAgcgagcga                                                                                                              <  1:206684/140‑1 (MQ=255)

                       cGTATCGGTGCTCAACAAAGTTATGAACGTTGTTGGCAACCGCCAGTTTGAACAGTGCCGTGGCGCTGTCCAAATCCCCCAGACTTAGGTAGTACTTACCTAAATAGAAGTTGGCTTCACTGAGATGCTCAGcgagcgag                                                                                                             >  1:844873/1‑140 (MQ=255)

                                    aacaaAGTTATGAACGTTGTTGGCAACCGCCAGTTTGAACAGTGCCGTGGCGCTGTCCAAATCCCCCAGACTTAGGTAGTACTTACCTAAATAGAAGTTGGCTTCACTGAGATGCTCAGCGAGCGAGGTGTTATCCGTTg                                                                                                >  1:672619/1‑140 (MQ=255)

                                       aaaGTTATGAACGTTGTTGGCAACCGCCAGTTTGAACAGTGCCGTGGCGCTGTCCAAATCCCCCAGACTTAGGTAGTACTTACCTAAATAGAAGTTGGCTTCACTGAGATGCTCAGCGAGCGAGGTGTTATCCGTTGCGt                                                                                             <  2:433372/140‑1 (MQ=255)

                                        aaGTTATGAACGTTGTTGGCAACCGCCAGTTTGAACAGTGCCGTGGCGCTGTCCAAATCCCCCAGACTTAGGTAGTACTTACCTAAATAGAAGTTGGCTTCACTGAGATGCTCAGCGAGCGAGGTGTTATCCGTTGCGTc                                                                                            <  2:339344/140‑1 (MQ=255)

                                         aGTTATGAACGTTGTTGGCAACCGCCAGTTTGAACAGTGCCGTGGCGCTGTCCAAATCCCCCAGACTTAGGTAGTACTTACCTAAATAGAAGTTGGCTTCACTGAGATGCTCAGCGAGCGAGGTGTTATCCGTTGCGTcc                                                                                           >  1:902326/1‑140 (MQ=255)

                                                     tgttgGCAACCGCCAGTTTGAACAGTGCCGTGGCGCTGTCCAAATCCCCCAGACTTAGGTAGTACTTACCTAAATAGAAGTTGGCTTCACTGAGATGCTCAGCGAGCGAGGTGTTATCCGTTGCGTCCGCCTTGAGCCt                                                                                >  2:691095/1‑139 (MQ=255)

                                                     tgttgGCAACCGCCAGTTTGAACAGTGCCGTGGCGCTGTCCAAATCCCCCAGACTTAGGTAGTACTTACCTAAATAGAAGTTGGCTTCACTGAGATGCTCAGCGAGCGAGGTGTTATCCGTTGCGTCCGCCTTGAGCCt                                                                                <  1:691095/139‑1 (MQ=255)

                                                                     tttGAACAGTGCCGTGGCGCTGTCCAAATCCCCCAGACTTAGGTAGTACTTACCTAAATAGAAGTTGGCTTCACTGAGATGCTCAGCGAGCGAGGTGTTATCCGTTGCGTCCGCCTTGAGCCTTTCCATTAACGTTTg                                                                 >  1:136635/1‑138 (MQ=255)

                                                                     tttGAACAGTGCCGTGGCGCTGTCCAAATCCCCCAGACTTAGGTAGTACTTACCTAAATAGAAGTTGGCTTCACTGAGATGCTCAGCGAGCGAGGTGTTATCCGTTGCGTCCGCCTTGAGCCTTTCCATTAACGTTTg                                                                 <  2:136635/138‑1 (MQ=255)

                                                                              tGCCGTGGCGCTGTCCAAATCCCCCAGACTTAGGTAGTACTTACCTAAATAGAAGTTGGCTTCACTGAGATGCTCAGCGAGCGAGGTGTTATCCGTTGCGTCCGCCTTGAGCCTTTCCATTAACGTTTGTTCGCTAATGt                                                      >  2:56782/1‑140 (MQ=255)

                                                                              tGCCGTGGCGCTGTCCAAATCCCCCAGACTTAGGTAGTACTTACCTAAATAGAAGTTGGCTTCACTGAGATGCTCAGCGAGCGAGGTGTTATCCGTTGCGTCCGCCTTGAGCCTTTCCATTAACGTTTGTTCGCTAATGt                                                      >  2:466653/1‑140 (MQ=255)

                                                                                 cGTGGCGCTGTCCAAATCCCCCAGACTTAGGTAGTACTTACCTAAATAGAAGTTGGCTTCACTGAGATGCTCAGCGAGCGAGGTGTTATCCGTTGCGTCCGCCTTGAGCCTTTCCATTAACGTTTGTTCGCTAATGTTGc                                                   <  2:669672/140‑1 (MQ=255)

                                                                                 cGTGGCGCTGTCCAAATCCCCCAGACTTAGGTAGTACTTACCTAAATAGAAGTTGGCTTCACTGAGATGCTCAGCGAGCGAGGTGTTATCCGTTGCGTCCGCCTTGAGCCTTTCCATTAACGTTTGTTCGCTAATGTTGc                                                   >  2:771178/1‑140 (MQ=255)

                                                                                  gTGGCGCTGTCCAAATCCCCCAGACTTAGGTAGTACTTACCTAAATAGAAGTTGGCTTCACTGAGATGCTCAGCGAGCGAGGTGTTATCCGTTGCGTCCGCCTTGAGCCTTTCCATTAACGTTTGTTCGCTAATGTTGcc                                                  <  2:844873/140‑1 (MQ=255)

                                                                                        cTGTCCAAATCCCCCAGACTTAGGTAGTACTTACCTAAATAGAAGTTGGCTTCACTGAGATGCTCAGCGAGCGAGGTGTTATCCGTTGCGTCCGCCTTGAGCCTTTCCATTAACGTTTGTTCGCTAATGTTGCCCAGGTa                                            >  2:723707/1‑140 (MQ=255)

                                                                                                  cccccAGACTTAGGTAGTACTTACCTAAATAGAAGTTGGCTTCACTGAGATGCTCAGCGAGCGAGGTGTTATCCGTTGCGTCCGCCTTGAGCCTTTCCATTAACGTTTGTTCGCTAATGTTGCCCAGGTAGAACTCGACa                                  <  1:771178/140‑1 (MQ=255)

                                                                                                  cccccAGACTTAGGTAGTACTTACCTAAATAGAAGTTGGCTTCACTGAGATGCTCAGCGAGCGAGGTGTTATCCGTTGCGTCCGCCTTGAGCCTTTCCATTAACGTTTGTTCGCTAATGTTGCCCAGGTAGAACTCGACa                                  <  1:461285/140‑1 (MQ=255)

                                                                                                     ccAGACTTAGGTAGTACTTACCTAAATAGAAGTTGGCTTCACTGAGATGCTCAGCGAGCGAGGTGTTATCCGTTGCGTCCGCCTTGAGCCTTTCCATTAACGTTTGTTCGCTAATGTTGCCCAGGTAg                                           <  1:654251/128‑1 (MQ=255)

                                                                                                     ccAGACTTAGGTAGTACTTACCTAAATAGAAGTTGGCTTCACTGAGATGCTCAGCGAGCGAGGTGTTATCCGTTGCGTCCGCCTTGAGCCTTTCCATTAACGTTTGTTCGCTAATGTTGCCCAGGTAg                                           >  2:654251/1‑128 (MQ=255)

                                                                                                     ccAGACTTAGGTAGTACTTACCTAAATAGAAGTTGGCTTCACTGAGATGCTCAGCGAGCGAGGTGTTATCCGTTGCGTCCGCCTTGAGCCTTTCCATTAACGTTTGTTCGCTAATGTTGCCCAGGTAGAACt                                       <  1:440350/132‑1 (MQ=255)

                                                                                                     ccAGACTTAGGTAGTACTTACCTAAATAGAAGTTGGCTTCACTGAGATGCTCAGCGAGCGAGGTGTTATCCGTTGCGTCCGCCTTGAGCCTTTCCATTAACGTTTGTTCGCTAATGTTGCCCAGGTAGAACt                                       >  2:440350/1‑132 (MQ=255)

                                                                                                     ccAGACTTAGGTAGTACTTACCTAAATAGAAGTTGGCTTCACTGAGATGCTCAGCGAGCGAGGTGTTATCCGTTGCGTCCGCCTTGAGCCTTTCCATTAACGTTTGTTCGCTAATGTTGCCCAGGTAGAACTCGACAATg                               >  2:286299/1‑140 (MQ=255)

                                                                                                     ccAGACTTAGGTAGTACTTACCTAAATAGAAGTTGGCTTCACTGAGATGCTCAGCGAGCGAGGTGTTATCCGTTGCGTCCGCCTTGAGCCTTTCCATTAACGTTTGTTCGCTAATGTTGCCCAGGTAGAACTCGACAATg                               >  2:823763/1‑140 (MQ=255)

                                                                                                     ccAGACTTAGGTAGTACTTACCTAAATAGAAGTTGGCTTCACTGAGATGCTCAGCGAGCGAGGTGTTATCCGTTGCGTCCGCCTTGAGCCTTTCCATTAACGTTTGTTCGCTAATGTTGCCCAGGTAGAACTCGACAATg                               >  2:512170/1‑140 (MQ=255)

                                                                                                                   taCTTACCTAAATAGAAGTTGGCTTCACTGAGATGCTCAGCGAGCGAGGTGTTATCCGTTGCGTCCGCCTTGAGCCTTTCCATTAACGTTTGTTCGCTAATGTTGCCCAGCTAGAACTCGACAATGTTCCATCCCCACTg                 >  1:673030/1‑140 (MQ=255)

                                                                                                                     cTTACCTAAATAGAAGTTGGCTTCACTGAGATGCTCAGCGAGCGAGGTGTTATCCGTTGCGTCCGCCTTGAGCCTTTCCATTAACGTTTGTTCGCTAATGTTGCCCAGGTAGAACTCGACAATGTTCCATCCCCACTGtt               >  1:417506/1‑140 (MQ=255)

                                                                                                                        aCCTAAATAGAAGTTGGCTTCACTGAGATGCTCAGCGAGCGAGGTGTTATCCGTTGCGTCCGCCTTGAGCCTTTCCATTAACGTTTGTTCGCTAATGTTGCCCAGGTAGAACTCGACAATGTTCCATCCCCACt                  <  2:90286/134‑1 (MQ=255)

                                                                                                                        aCCTAAATAGAAGTTGGCTTCACTGAGATGCTCAGCGAGCGAGGTGTTATCCGTTGCGTCCGCCTTGAGCCTTTCCATTAACGTTTGTTCGCTAATGTTGCCCAGGTAGAACTCGACAATGTTCCATCCCCACt                  >  1:90286/1‑134 (MQ=255)

                                                                                                                            aaaTAGAAGTTGGCTTCACTGAGATGCTCAGCGAGCGAGGTGTTATCCGTTGCGTCCGCCTTGAGCCTTTCCATTAACGTTTGTTCGCTAATGTTGCCCAGGTAGAACTCGACAATGTTCCATCCCCACTGTTCCTTATc        >  2:376132/1‑140 (MQ=255)

                                                                                                                             aaTAGAAGTTGGCTTCACTGAGATGCTCAGCGAGCGAGGTGTTATCCGTTGCGTCCGCCTTGAGCCTTTCCATTAACGTTTGTTCGCTAATGTTGCCCAGGTAGAACTCGACAATGTTCCATCCCCACTGTTCCTTATcc       >  1:882699/1‑140 (MQ=255)

                                                                                                                             aaTAGAAGTTGGCTTCACTGAGATGCTCAGCGAGCGAGGTGTTATCCGTTGCGTCCGCCTTGAGCCTTTCCATTAACGTTTGTTCGCTAATGTTGCCCAGGTAGAACTCGACAATGTTCCATCCCCACTGTTCCTTATcc       >  1:593835/1‑140 (MQ=255)

                                                                                                                                  aaGTTGGCTTCACTGAGATGCTCAGCGAGCGAGGTGTTATCCGTTGCGTCCGCCTTGAGCCTTTCCATTAACGTTTGTTCGCTAATGTTGCCCAGGTAGAACTCGACAATGTTCCATCCCCACTGTTCCTTATCCGAttt  >  1:663416/1‑140 (MQ=255)

                                                                                                                                  aaGTTGGCTTCACTGAGATGCTCAGCGAGCGAGGTGTTATCCGTTGCGTCCGCCTTGAGCCTTTCCATTAACGTTTGTTCGCTAATGTTGCCCAGGTAGAACTCGACAATGTTCCATCCCCACTGTTCCTTATCCGAttt  >  1:454009/1‑140 (MQ=255)

CAGGAGCGATAATTCCAACAATGCGTATCGGTGCTCAACAAAGTTATGAACGTTGTTGGCAACCGCCAGTTTGAACAGTGCCGTGGCGCTGTCCAAATCCCCCAGACTTAGGTAGTACTTACCTAAATAGAAGTTGGTTTCACTGAGATGCTCAGCGAGCGAGGTGTTATCCGTTGCGTCCGCCTTGAGCCTTTCCATTAACGTTTGTTCGCTAATGTTGCCCAGGTAGAACTCGACAATGTTCCATCCCCACTGTTCCTTATCCGATTT  >  NC_000913/3308082‑3308351

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A