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
A4 F1 I2 R1	780	68.3	3343050	93.5%	3125751	102.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,089,570	T→C	E96E (GAA→GAG)	pgaB ←	poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine (PGA) N‑deacetylase outer membrane export lipoprotein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,089,570	0	T	C	100.0%	122.1 / NA	35	E96E (GAA→GAG)	pgaB	poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine (PGA) N‑deacetylase outer membrane export lipoprotein
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (17/18); total (17/18)

CAGGCCACTGGAAGGCCTGAAGAATTGGGAAGACGCGGGTATAAAAACTCTGGTAGCCGTCATCAAAAGTCAGCACTACAGCTTTTTCCGGTAGCGGTTTTCCTCCTCGATGTGCTTCACGAATTTGAGCAATACTGACCGGTTGATAACCGTTCTCGCGCAGCCAGGCAAATTGTTCACGCAGTGCTGATGTCCGCACTGACATAAAACGCTGGTCGGCAGCTTCGTCTTCAACGTTATGCCATGAAA  >  NC_000913/1089455‑1089703

cagGCCACTGGAAGGCCTGAAGAATTGGGAAGACGCGGGTATAAAAACTCTGGTAGCCGTCATCAAAAGTCAGCACTACAGCTTTTTCCGGTAGCGGTTTTCCTCCTCGATGTGCCTCACGAAt                                                                                                                               <  2:1497007/124‑1 (MQ=255)

cagGCCACTGGAAGGCCTGAAGAATTGGGAAGACGCGGGTATAAAAACTCTGGTAGCCGTCATCAAAAGTCAGCACTACAGCTTTTTCCGGTAGCGGTTTTCCTCCTCGATGTGCCTCACGAAt                                                                                                                               >  1:1497007/1‑124 (MQ=255)

cagGCCACTGGAAGGCCTGAAGAATTGGGAAGACGCGGGTATAAAAACTCTGGTAGCCGTCATCAAAAGTCAGCACTACAGCTTTTTCCGGTAGCGGTTTTCCTCCTCGATGTGCCTCACGAATTTGAGCAATACTGAc                                                                                                                <  1:454159/139‑1 (MQ=255)

cagGCCACTGGAAGGCCTGAAGAATTGGGAAGACGCGGGTATAAAAACTCTGGTAGCCGTCATCAAAAGTCAGCACTACAGCTTTTTCCGGTAGCGGTTTTCCTCCTCGATGTGCCTCACGAATTTGAGCAATACTGAc                                                                                                                >  2:1363591/1‑139 (MQ=255)

   gCCACTGGAAGGCCTGAAGAATTGGGAAGACGCGGGTATAAAAACTCTGGTAGCCGTCATCAAAAGTCAGCACTACAGCTTTTTCCGGTAGCGGTTTTCCTCCTCGATGTGCCTCACGAATTTGAg                                                                                                                          <  2:572259/126‑1 (MQ=255)

   gCCACTGGAAGGCCTGAAGAATTGGGAAGACGCGGGTATAAAAACTCTGGTAGCCGTCATCAAAAGTCAGCACTACAGCTTTTTCCGGTAGCGGTTTTCCTCCTCGATGTGCCTCACGAATTTGAg                                                                                                                          >  1:572259/1‑126 (MQ=255)

   gCCACTGGAAGGCCTGAAGAATTGGGAAGACGCGGGTATAAAAACTCTGGTAGCCGTCATCAAAAGTCAGCACTACAGCTTTTTCCGGTAGCGGTTTTCCTCCTCGATGTGCCTCACGAATTTGAGCAATACTGACCgg                                                                                                             >  1:885584/1‑139 (MQ=255)

             ggCCTGAAGAATTGGGAAGACGCGGGTATAAAAACTCTGGTAGCCGTCATCAAAAGTCAGCACTACAGCTTTTTCCGGTAGCGGTTTTCCTCCTCGATGTGCCTCACGAATTTGAGCAATACTGACCGGTTGATAACCg                                                                                                   >  1:184302/1‑139 (MQ=255)

                         tGGGAAGACGCGGGTATAAAAACTCTGGTAGCCGTCATCAAAAGTCAGCACTACAGCTTTTTCCGGTAGCGGTTTTCCTCCTCGATGTGCCTCACGAATTTGAGCAATACTGACCGGTTGATAACCGTTCTCGCGCAGc                                                                                       <  2:488156/139‑1 (MQ=255)

                                aCGCGGGTATAAAAACTCTGGTAGCCGTCATCAAAAGTCAGCACTACAGCTTTTTCCGGTAGCGGTTTTCCTCCTCGATGTGCCTCACGAAt                                                                                                                               >  1:1648705/1‑92 (MQ=255)

                                aCGCGGGTATAAAAACTCTGGTAGCCGTCATCAAAAGTCAGCACTACAGCTTTTTCCGGTAGCGGTTTTCCTCCTCGATGTGCCTCACGAAt                                                                                                                               <  2:1648705/92‑1 (MQ=255)

                                     ggTATAAAAACTCTGGTAGCCGTCATCAAAAGTCAGCACTACAGCTTTTTCCGGTAGCGGTTTTCCTCCTCGATGTGCCTCACGAATTTGAGCAATACTGACCGGTTGATAACCGTTCTCGCGCAGCCAGGCAAATTGt                                                                           >  1:731951/1‑139 (MQ=255)

                                       tataAAAACTCTGGTAGCCGTCATCAAAAGTCAGCACTACAGCTTTTTCCGGTAGCGGTTTTCCTCCTCGATGTGCCTCACGAATTTGAGCAATACTGACCGGTTGATAACCGTTCTCGCGCAGCCAGGCAAATTGTTc                                                                         >  1:1562560/1‑139 (MQ=255)

                                          aaaaaCTCTGGTAGCCGTCATCAAAAGTCAGCACTACAGCTTTTTCCGGTAGCGGTTTTCCTCCTCGATGTGCCTCACGAATTTGAGCAATACTGACCGGTTGATAACCGTTCTCGCGCAGCCAGGCAAATTGTTCACg                                                                      <  1:1363591/139‑1 (MQ=255)

                                          aaaaaCTCTGGTAGCCGTCATCAAAAGTCAGCACTACAGCTTTTTCCGGTAGCGGTTTTCCTCCTCGATGTGCCTCACGAATTTGAGCAATACTGACCGGTTGATAACCGTTCTCGCGCAGCCAGGCAAATTGTTCACg                                                                      <  2:1562560/139‑1 (MQ=255)

                                          aaaaaCTCTGGTAGCCGTCATCAAAAGTCAGCACTACAGCTTTTTCCGGTAGCGGTTTTCCTCCTCGATGTGCCTCACGAATTTGAGCAATACTGACCGGTTGATAACCGTTCTCGCGCAGCCAGGCAAATTGTTCACg                                                                      <  2:731951/139‑1 (MQ=255)

                                          aaaaaCTCTGGTAGCCGTCATCAAAAGTCAGCACTACAGCTTTTTCCGGTAGCGGATTTCCTCCTCGATGTGCCTCACGAATTTGAGCAATACTGACCGGTTGATAACCGTTCTCGCGCAGCCAGGCAAATTGTTCACg                                                                      <  2:885584/139‑1 (MQ=255)

                                                tctGGTAGCCGTCATCAAAAGTCAGCACTACAGCTTTTTCCGGTAGCGGTTTTCCTCCTCGATGTGCCTCACGAATTTGAGCAATACTGACCGGTTGATAACCGTTCTCGCGCAGCCAGGCAAATTGTTCACg                                                                      >  1:1261423/1‑133 (MQ=255)

                                                tctGGTAGCCGCCATCAAAAGTCAGCACTACAGCTTTTTCCGGTAGCGGTTTTCCTCCTCGATGTGCCTCACGAATTTGAGCAATACTGACCGGTTGATAACCGTTCTCGCGCAGCCAGGCAAATTGTTCACg                                                                      <  2:1261423/133‑1 (MQ=255)

                                                    gTAGCCGTCATCAAAAGTCAGCACTACAGCTTTTTCCGGTAGCGGTTTTCCTCCTCGATGTGCCTCACGAAt                                                                                                                               >  2:1180567/1‑72 (MQ=255)

                                                    gTAGCCGTCATCAAAAGTCAGCACTACAGCTTTTTCCGGTAGCGGTTTTCCTCCTCGATGTGCCTCACGAAt                                                                                                                               <  1:1180567/72‑1 (MQ=255)

                                                    gTAGCCGTCATCAAAAGTCAGCACTACAGCTTTTTCCGGTAGCGGTTTTCCTCCTCGATGTGCCTCACGAATTTGAGCAATACTg                                                                                                                  <  2:585258/85‑1 (MQ=255)

                                                    gTAGCCGTCATCAAAAGTCAGCACTACAGCTTTTTCCGGTAGCGGTTTTCCTCCTCGATGTGCCTCACGAATTTGAGCAATACTg                                                                                                                  >  1:585258/1‑85 (MQ=255)

                                                           tcatcaAAAGTCAGCACTACAGCTTTTTCCGGTAGCGGTTTTCCTCCTCGATGTGCCTCACGAATTTGAGCAATACTGACCGGTTGATAACCGTTCTCGCGCAGCCAGGCAAATTGTTCACGCAGTGCTGATGTCCGCa                                                     <  2:184302/139‑1 (MQ=255)

                                                            catcaAAAGTCAGCACTACAGCTTTTTCCGGTAGCGGTTTTCCTCCTCGATGTGCCTCACGAATTTGAGCAATACTGAcc                                                                                                               >  1:170057/1‑80 (MQ=255)

                                                            catcaAAAGTCAGCACTACAGCTTTTTCCGGTAGCGGTTTTCCTCCTCGATGTGCCTCACGAATTTGAGCAATACTGAcc                                                                                                               <  2:170057/80‑1 (MQ=255)

                                                                       aGCACTACAGCTTTTTCCGGTAGCGGTTTTCCTCCTCGATGTGCCTCACGAATTTGAGCAATACTGACCGGTTGATAACCGTTCTCGCGCAGCCAGGCAAATTGTTCACGCAGTGCTGATGTCCGCACTGACATAAAAc                                         >  1:890511/1‑139 (MQ=255)

                                                                         cACTACAGCTTTTTCCGGTAGCGGTTTTCCTCCTCGATGTGCCTCACGAATTTGAGCAATACTGACCGGTTGATAACCGTTCTCGCGCAGCCAGGCAAATTGTTCACGCAGTGCTGATGTCCg                                                       <  2:1053661/123‑1 (MQ=255)

                                                                         cACTACAGCTTTTTCCGGTAGCGGTTTTCCTCCTCGATGTGCCTCACGAATTTGAGCAATACTGACCGGTTGATAACCGTTCTCGCGCAGCCAGGCAAATTGTTCACGCAGTGCTGATGTCCg                                                       >  1:1053661/1‑123 (MQ=255)

                                                                                     ttCCGGTAGCGGTTTTCCTCCTCGATGTGCCTCACGAATTTGAGCAATACTGACCGGTTGATAACCGTTCTCGCGCAGCCAGGCAAATTGTTCACGCAGTGCTGATGTCCGCACTGACATAAAACGCTGGTCGGCAGCt                           <  1:822143/139‑1 (MQ=255)

                                                                                                   ttCCTCCTCGATGTGCCTCACGAATTTGAGCAATACTGACCGGTTGATAACCGTTCTcgcg                                                                                           >  2:1059454/1‑61 (MQ=255)

                                                                                                   ttCCTCCTCGATGTGCCTCACGAATTTGAGCAATACTGACCGGTTGATAACCGTTCTcgcg                                                                                           <  1:1059454/61‑1 (MQ=255)

                                                                                                           cGATGTGCCTCACGAATTTGAGCAATACTGACCGGTTGATAACCGTTCTCGCGCAGCCAGGCAAATTGTTCACg                                                                      <  1:858047/74‑1 (MQ=255)

                                                                                                           cGATGTGCCTCACGAATTTGAGCAATACTGACCGGTTGATAACCGTTCTCGCGCAGCCAGGCAAATTGTTCACg                                                                      >  2:858047/1‑74 (MQ=255)

                                                                                                              tgtgCCTCACGAATTTGAGCAATACTGACCGGTTGATAACCGTTCTCGCGCAGCCAGGCAAATTGTTCACGCAGTGCTGATGTCCGCACTGACATAAAACGCTGGTCGGCAGCTTCGTCTTCAACGTTATGCCATGaaa  >  2:583271/1‑139 (MQ=255)

CAGGCCACTGGAAGGCCTGAAGAATTGGGAAGACGCGGGTATAAAAACTCTGGTAGCCGTCATCAAAAGTCAGCACTACAGCTTTTTCCGGTAGCGGTTTTCCTCCTCGATGTGCTTCACGAATTTGAGCAATACTGACCGGTTGATAACCGTTCTCGCGCAGCCAGGCAAATTGTTCACGCAGTGCTGATGTCCGCACTGACATAAAACGCTGGTCGGCAGCTTCGTCTTCAACGTTATGCCATGAAA  >  NC_000913/1089455‑1089703

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A