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
A12 F1 I2 R1	766	55.6	2631458	94.7%	2491990	109.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,308,868	G→A	C19C (TGC→TGT)	nlpI ←	lipoprotein involved in osmotic sensitivity and filamentation

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,308,868	0	G	A	100.0%	111.7 / NA	35	C19C (TGC→TGT)	nlpI	lipoprotein involved in osmotic sensitivity and filamentation
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (16/19); total (16/19)

GCTGTGCGCGTTCGTCATCGGTTAAAGCCCGACTGGCAAGGATTTGTTCCATACGTGCCAGAATCACTTCCTGCTGTAAAGTCGGTTGCAATGGTACCGCGAGGACTTCACTTTTACGCCAGGAAGTATTACTGCATCCTGCAAGCGTAAGTGCTGTCGCAACGAAACACCAGCGC‑AAAAAAGGCTTCATTTCCCACTCCCGAAGACCACGGTTGAATGAACGTCCTGTTCCCGGTTGCTAACAAGGCGTCCTGCCCGGTTAAAAGC  >  NC_000913/3308735‑3309001

gCTGTGCGCGTTCGTCATCGGTTAAAGCCCGACTGGCAAGGATTTGTTCCATACGTGCCAGAATCACTTCCTGCTGTAAAGTCGGTTGCAATGGTACCGCGAGGACTTCACTTTTACGCCAGGAAGTATTACTACATcc                                                                                                                                   >  1:745266/1‑139 (MQ=255)

   gtgCGCGTTCGTCATCGGTTAAAGCCCGACTGGCAAGGATTTGTTCCATACGTGCCAGAATCACTTCCTGCTGTAAAGTCGGTTGCAATGGTACCGCGAGGACTTCACTTTTACGCCAGGAAGTATTACTACATCCTGc                                                                                                                                >  1:743503/1‑139 (MQ=255)

                       aaaGCCCGACTGGCAAGGATTTGTTCCATACGTGCCAGAATCACTTCCTGCTGTAAAGTCGGTTGCAATGGTACCGCGAGGACTTCACTTTTACGCCAGGAAGTATTACTACATCCTGCAAGCGTAAGTGCTGTCGCaa                                                                                                            <  2:1151736/139‑1 (MQ=255)

                             cGACTGGCAAGGATTTGTTCCATACGTGCCAGAATCACTTCCTGCTGTAAAGTCGGTTGCAATGGTACCGCGAGGACTTCACTTTTACGCCAGGAAGTATTACTACATCCTGCAAGCGTAAGTGCTGTCGCAACGAAac                                                                                                      >  1:528430/1‑139 (MQ=255)

                                            tGTTCCATACGTGCCAGAATCACTTCCTGCTGTAAAGTCGGTTGCAATGGTACCGCGAGGACTTCACTTTTACGCCAGGAAGTATTACTACATCCTGCAAGCGTAAGTGCTGTCGCAACGAAACACCAGCGC‑AAAAAAg                                                                                      >  2:410796/1‑139 (MQ=255)

                                            tGTTCCATACGTGCCAGAATCACTTCCTGCTGTAAAGTCGGTTGCAATGGTACCGCGAGGACTTCACTTTTACGCCAGGAAGTATTACTACATCCTGCAAGCGTAAGTGCTGTCGCAACGAAACACCAGCGC‑AAAAAAg                                                                                      >  1:3081/1‑139 (MQ=255)

                                                        gCCAGAATCACTTCCTGCTGTAAAGTCGGTTGCAATGGTACCGCGAGGACTTCACTTTTACGCCAGGAAGTATTACTACATCCTGCAAGCGTAAGTGCTGTCGCAACGAAACACCAGCGC‑AAAAAAGGCTTCATTTccc                                                                          >  2:409478/1‑139 (MQ=255)

                                                        gCCAGAATCACTTCCTGCTGTAAAGTCGGTTGCAATGGTACCGCGAGGACTTCACTTTTACGCCAGGAAGTATTACTACATCCTGCAAGCGTAAGTGCTGTCGCAACGAAACACCAGCGC‑AAAAAAGGCTTCATTTccc                                                                          >  1:554771/1‑139 (MQ=255)

                                                         ccAGAATCACTTCCTGCTGTAAAGTCGGTTGCAATGGTACCGCGAGGACTTCACTTTTACGCCAGGAAGTATTACTACATCCTGCAAGCGTAAGTGCTGTCGCAACGAAACACCAGCGC‑AAAAAAGGCTTCATTTCCCa                                                                         <  1:410796/139‑1 (MQ=255)

                                                         ccAGAATCACTTCCTGCTGTAAAGTCGGTTGCAATGGTACCGCGAGGACTTCACTTTTACGCCAGGAAGTATTACTACATCCTGCAAGCGTAAGTGCTGTCGCAACGAAACACCAGCGC‑AAAAAAGGCTTCATTTCCCa                                                                         <  2:554771/139‑1 (MQ=255)

                                                             aaTCACTTCCTGCTGTAAAGTCGGTTGCAATGGTACCGCGAGGACTTCACTTTTACGCCAGGAAGTATTACTACATCCTGCAAGCGTAAGTGCTGTCGCAACGAAACACCAGCGC‑AAAAAAGGCTTCATTTCCCACTcc                                                                     >  2:299440/1‑139 (MQ=255)

                                                               tCACTTCCTGCTGTAAAGTCGGTTGCAATGGTACCGCGAGGACTTCACTTTTACGCCAGGAAGTATTACTACATCCTGCAAGCGTAAGTGCTGTCGCAACGAAACACCAGCGC‑AAAAAAGGCTTCATTTCCCACTCCCg                                                                   <  1:409478/139‑1 (MQ=255)

                                                                 aCTTCCTGCTGTAAAGTCGGTTGCAATGGTACCGCGAGGACTTCACTTTTACGCCAGGAAGTATTACTACATCCTGCAAGCGTAAGTGCTGTCGCAACGAAACACCAGCGC‑AAAAAAGGCTTCATTTCCCACTCCCGaa                                                                 <  1:183315/139‑1 (MQ=255)

                                                                   ttCCTGCTGTAAAGTCGGTTGCAATGGTACCGCGAGGACTTCACTTTTACGCCAGGAAGTATTACTACATCCTGCAAGCGTAAGTGCTGTCg                                                                                                               >  1:1278268/1‑92 (MQ=255)

                                                                   ttCCTGCTGTAAAGTCGGTTGCAATGGTACCGCGAGGACTTCACTTTTACGCCAGGAAGTATTACTACATCCTGCAAGCGTAAGTGCTGTCg                                                                                                               <  2:1278268/92‑1 (MQ=255)

                                                                      ctgctgTAAAGTCGGTTGCAATGGTACCGCGAGGACTTCACTTTTACGCCAGGAAGTATTACTACATCCTGCAAGCGTAAGTGCTGTCGCAACGAAACACCAGCGC‑AAAAAAGGCTTCATTTCCCACTCCCGAAGACCa                                                            <  2:528430/139‑1 (MQ=255)

                                                                       tgctgTAAAGTCGGTTGCAATGGTACCGCGAGGACTTCACTTTTACGCCAGGAAGTATTACTACATCCTGCAAGCGTAAGTGCTGTCGCAACGAAACACCAGCGC‑AAAAAAGGCTTCATTTCCCACTCCCGAAGACCAc                                                           >  1:1302305/1‑139 (MQ=255)

                                                                          tgTAAAGTCGGTTGCAATGGTACCGCGAGGACTTCACTTTTACGCCAGGAAGTATTACTACATCCTGCAAGCGTAAGTGCTGTCGCAACGAAACACCAGCGCAAAAAAAGGCTTCATTTCCCACTCCCGAAGACCACgg                                                         <  2:496940/139‑1 (MQ=255)

                                                                              aaGTCGGTTGCAATGGTACCGCGAGGACTTCACTTTTACGCCAGGAAGTATTACTACAt                                                                                                                                     >  1:818246/1‑59 (MQ=255)

                                                                              aaGTCGGTTGCAATGGTACCGCGAGGACTTCACTTTTACGCCAGGAAGTATTACTACAt                                                                                                                                     <  2:818246/59‑1 (MQ=255)

                                                                                  cGGTTGCAATGGTACCGCGAGGACTTCACTTTTACGCCAGGAAGTATTACTACATCCTGCAAGCGTAAGTGCTGTCGCAACGAAACACCAGCGC‑AAAAAAGGCTTCATTTCCCACTCCCGAAGACCACGGTtgaatgaa                                                <  2:1302305/139‑1 (MQ=255)

                                                                                      tGCAATGGTACCGCGAGGACTTCACTTTTACGCCAGGAAGTATTACTACATCCTGCAAGCGTAAGTGCTGTCGCAACGAAACACCAGCGC‑AAAAAAGGCTTCATTTCCCACTCCCGAAGACCACGGTTGAATGAACGTc                                            <  1:499626/139‑1 (MQ=255)

                                                                                              tACCGCGAGGACTTCACTTTTACGCCAGGAAGTATTACTACATCCTGCAAGCGTAAGTGCTGTCGCAACGAAACACCAGCGC‑AAAAAAGGCTTCATTTCCCACTCCCGAAGACCACGGTTGAATGAACGTCCTGTTccc                                    <  1:230418/139‑1 (MQ=255)

                                                                                                   cgAGGACTTCACTTTTACGCCAGGAAGTATTACTACATCCTGCAAGCGTAAGTGCTGTCGCAACGAAACACCAGCGC‑AAAAAAGGCTTCATTTCCCACTCCCGAAGACCACGGTTGAATGAACGTc                                            >  1:1118658/1‑126 (MQ=255)

                                                                                                   cgAGGACTTCACTTTTACGCCAGGAAGTATTACTACATCCTGCAAGCGTAAGTGCTGTCGCAACGAAACACCAGCGC‑AAAAAAGGCTTCATTTCCCACTCCCGAAGACCACGGTTGAATGAACGTc                                            <  2:1118658/126‑1 (MQ=255)

                                                                                                   cgAGGACTTCACTTTTACGCCAGGAAGTATTACTACATCCTGCAAGCGTAAGTGCTGTCGCAACGAAACACCAGCGC‑AAAAAAGGCTTCATTTCCCACTCCCGAAGACCACGGTTGAATGAACGTCCTGTTCCCGGTTg                               >  2:824801/1‑139 (MQ=255)

                                                                                                     aGGACTTCACTTTTACGCCAGGAAGTATTACTACATCCTGCAAGCGTAAGTGCTGTCGCAACGAAACACCAGCGC‑AAAAAAGGCTTCATTTCCCACTCCCGAAGACCACGGTTGAATGAACGTCCTGTTCCCGGTTGCt                             <  2:193508/139‑1 (MQ=255)

                                                                                                        aCTTCACTTTTACGCCAGGAAGTATTACTACATCCTGCAAGCGTAAGTGCTGTCGCAACGAAACACCAGCGC‑AAAAAAGGCTTCATTTCCCACTCCCGAAGACCACGGTTGAATGAACGTCCTGTTCCCGGTTGCTAAc                          <  1:824801/139‑1 (MQ=255)

                                                                                                                    cGCCAGGAAGTATTACTACATCCTGCAAGCGTAAGTGCTGTCGCAACGAAacac                                                                                                    >  2:506931/1‑54 (MQ=255)

                                                                                                                    cGCCAGGAAGTATTACTACATCCTGCAAGCGTAAGTGCTGTCGCAACGAAacac                                                                                                    <  1:506931/54‑1 (MQ=255)

                                                                                                                      ccAGGAAGTATTACTACATCCTGCAAGCGTAAGTGCTGTCGCAACGAAACACCAGCGC‑AAAAAAGGCTTCATTTCCCACTCCCGAAGACCACGGTTGAATGAACGTCCTGTTCCCGGTTGCTAACAAGGCGTCCTGccc            <  2:743503/139‑1 (MQ=255)

                                                                                                                            aGTATTACTACATCCTGCAAGCGTAAGTGCTGTCGCAACGAAACACCAGCGC‑AAAAAAGGCTTCATTTCCCACTCCCGAAGACCACGGTTGAATGAACGTCCTGTTCCCGGTTGCTAACAAGGCGTCCTGCCCGGTTaa      <  1:411649/139‑1 (MQ=255)

                                                                                                                              tATTACTACATCCTGCAAGCGTAAGTGCTGTCGCAACGAAACACCAGCGC‑AAAAAAGGCTTCATTTCCCACTCCCg                                                                   >  1:811274/1‑76 (MQ=255)

                                                                                                                              tATTACTACATCCTGCAAGCGTAAGTGCTGTCGCAACGAAACACCAGCGC‑AAAAAAGGCTTCATTTCCCACTCCCg                                                                   <  2:811274/76‑1 (MQ=255)

                                                                                                                                ttACTACATCCTGCAAGCGTAAGTGCTGTCGCAACGAAACACCAGCGC‑AAAAAAGGCTTCATTTCCCACTCCCGAAGACCACGGTTGAATGAACGTCCTGTTCCCGGTTGCTAACAAGGCGTCCTGCCCGGTTAAAAGc  >  1:1009297/1‑139 (MQ=255)

GCTGTGCGCGTTCGTCATCGGTTAAAGCCCGACTGGCAAGGATTTGTTCCATACGTGCCAGAATCACTTCCTGCTGTAAAGTCGGTTGCAATGGTACCGCGAGGACTTCACTTTTACGCCAGGAAGTATTACTGCATCCTGCAAGCGTAAGTGCTGTCGCAACGAAACACCAGCGC‑AAAAAAGGCTTCATTTCCCACTCCCGAAGACCACGGTTGAATGAACGTCCTGTTCCCGGTTGCTAACAAGGCGTCCTGCCCGGTTAAAAGC  >  NC_000913/3308735‑3309001

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A