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 F28 I1 R1	163	52.9	1786516	99.3%	1774010	139.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,487,227	G→A	intergenic (+264/‑8)	hrpA → / → ydcF	ATP‑dependent RNA helicase HrpA/DUF218 domain‑containing protein YdcF

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,487,227	0	G	A	100.0%	132.8 / NA	38	intergenic (+264/‑8)	hrpA/ydcF	ATP‑dependent RNA helicase HrpA/DUF218 domain‑containing protein YdcF
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (22/16); total (22/16)

AATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTATTCTTAAGGGAACGATAAGGAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGTGGCTGGCGCAGGATGATTTCTCCGGTGAGGTGCCGTATCAGGCCGATTGCGTGATCCT  >  NC_000913/1487092‑1487359

aatGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTATTCTTAAGGGAACGATAAgaagga                                                                                                                                  <  1:625881/140‑1 (MQ=255)

 atGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATATGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTATTCTTAAGGGAACGATAAGAAGGaa                                                                                                                                 <  2:845191/140‑1 (MQ=255)

              gCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTATTCTTAAGGGAACGATAAGAAGGAACCATGAACATTAc                                                                                                                    <  1:664633/140‑1 (MQ=255)

                  ttCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTTAAGAAAAACAAATTTCTCCTTTTTGAGTGGTCCGCTTCTCCCTATTATTTCACCCAGTATTTTTTAGGGGAAGAAAAAAAAGAAACATGAAAAATAacccc                                                                                                                >  2:534613/1‑139 (MQ=255)

                                   cAGGCTTGCGGAGTGGCGGTTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTATTCTTAAGGGAACGATAAGAAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGcc                                                                                               <  1:242765/140‑1 (MQ=255)

                                   cAGGCTTGCGGAGTGGCGGTTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTATTCTTAAGGGAACGATAAGAAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGcc                                                                                               <  2:443159/140‑1 (MQ=255)

                                   cAGGCTTGCGGAGTGGCGGTTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTATTCTTAAGGGAACGATAAGAAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGcc                                                                                               <  1:534613/140‑1 (MQ=255)

                                     ggCTTGCGGAGTGGCGGTTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTATTCTTAAGGGAACGATAAGAAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCgg                                                                                             <  1:210921/140‑1 (MQ=255)

                                                          ggACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTATTCTTAAGGGAACGATAAGAAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATg                                                                        >  2:422547/1‑140 (MQ=255)

                                                                     ttCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTATTCTTAAGGGAACGATAAGAAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATaaa                                                                          >  1:329278/1‑127 (MQ=255)

                                                                     ttCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTATTCTTAAGGGAACGATAAGAAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATaaa                                                                          <  2:329278/127‑1 (MQ=255)

                                                                        ctcctTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTATTCTTAAGGGAACGATAAGAAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGtgg                                                          >  2:468409/1‑140 (MQ=255)

                                                                        ctcctTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTATTCTTAAGGGAACGATAAGAAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGtgg                                                          <  1:624388/140‑1 (MQ=255)

                                                                               cAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTATTCTTAAGGGAACGATAAGAAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGTGGCTGgcgc                                                   <  1:741790/140‑1 (MQ=255)

                                                                                     gCTCCGCTTCTCACTATTATCTCACGCAGTATTCTTAAGGGAACGATAAGAAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGTGGCTGGCGCAGgatg                                             >  1:703748/1‑140 (MQ=255)

                                                                                       tCCGCTTCTCACTATTATCTCACGCAGTATTCTTAAGGGAACGATAAGAAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGTGGCTGGCGCAGgatgat                                           >  1:499690/1‑140 (MQ=255)

                                                                                       tCCGCTTCTCACTATTATCTCACGCAGTATTCTTAAGGGAACGATAAGAAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGTGGCTGGCGCAGgatgat                                           >  2:467176/1‑140 (MQ=255)

                                                                                       tCCGCTTCTCACTATTATCTCACGCAGTATTCTTAAGGGAACGATAAGAAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGTGGCTGGCGCAGgatgat                                           >  2:290756/1‑140 (MQ=255)

                                                                                       tCCGCTTCTCACTATTATCTCACGCAGTATTCTTAAGGGAACGATAAGAAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGTGGCTGGCGCAGgatgat                                           >  1:560074/1‑140 (MQ=255)

                                                                                         cGCTTCTCACTATTATCTCACGCAGTATTCTTAAGGGAACGATAAGAAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGTGGCTGGCGCAGGATGAttt                                         <  1:852173/140‑1 (MQ=255)

                                                                                            ttCTCACTATTATCTCACGCAGTATTCTTAAGGGAACGATAAGAAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGTGGCTGGCGCGGGATGATTtctc                                      >  2:559815/1‑140 (MQ=255)

                                                                                            ttCTCACTATTATCTCACGCAGTATTCTTAAGGGAACGATAAGAAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGTGGCTGGCGCAGGATGATTtctc                                      >  1:802321/1‑140 (MQ=255)

                                                                                              ctcACTATTATCTCACGCAGTATTCTTAAGGGAACGATAAGAAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGTGGCTGGCGCAGGATGATTTCTCCg                                    >  2:470500/1‑140 (MQ=255)

                                                                                                  cTATTATCTCACGCAGTATTCTTAAGGGAACGATAAGAAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGTGGCTGGCGCAGGATGATTTCTCCGGTGa                                <  1:468409/140‑1 (MQ=255)

                                                                                                   tattatCTCACGCAGTATTCTTAAGGGAACGATAAGAAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGTGGCTGGCGCAGGATGATTTCTCCGGTGAg                               >  1:453913/1‑140 (MQ=255)

                                                                                                      tatCTCACGCAGTATTCTTAAGGGAACGATAAGAAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGTGGCTGGCGCAGGATGATTTCTCCGGTGAGGTg                            <  2:802321/140‑1 (MQ=255)

                                                                                                        tctcACGCAGTATTCTTAAGGGAACGATAAGAAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGTGGCTGGCGCAGgatga                                            <  2:628414/122‑1 (MQ=255)

                                                                                                        tctcACGCAGTATTCTTAAGGGAACGATAAGAAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGTGGCTGGCGCAGgatga                                            >  1:628414/1‑122 (MQ=255)

                                                                                                        tctcACGCAGTATTCTTAAGGGAACGATAAGAAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGTGGCTGGCGCAGGATGATTTCTCCGGTGAGGTGcc                          >  1:630507/1‑140 (MQ=255)

                                                                                                            aCGCAGTATTCTTAAGGGAACGATAAGAAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGTGGCTGGCGCAGGATGATTTCTCaggtgaggtg                            <  1:799237/134‑1 (MQ=255)

                                                                                                            aCGCAGTATTCTTAAGGGAACGATAAGAAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGTGGCTGGCGCAGGATGATTTCTCaggtgaggtg                            >  2:799237/1‑134 (MQ=255)

                                                                                                             cGCAGTATTCTTAAGGGAACGATAAGAAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGTGGCTGGCGCAGGATGATTTCTCCGGTGAGGTGCCGTATc                     >  1:750651/1‑140 (MQ=255)

                                                                                                             cGCAGTATTCTTAAGGGAACGATAAGAAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGTGGCTGGCGCAGGATGATTTCTCCGGTGAGGTGCCGTATc                     >  1:370757/1‑140 (MQ=255)

                                                                                                               cAGTATTCTTAAGGGAACGATAAGAAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGTGGCTGGCGCAGGATGATTTCTCCGGTGAGGTGCCGTATCAg                   >  2:187126/1‑140 (MQ=255)

                                                                                                                 gTATTCTTAAGGGAACGATAAGAAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGTGGCTGGCGCAGGATGATTTCTCCGGTGAGGTGCCATATCAGGc                 <  1:182594/140‑1 (MQ=255)

                                                                                                                           gggAACGATAAGAAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGTGGCTGGCGCAGGATGATTTCTCCGGTGAGGTGCCGTATCAGGCCGATTGCGTg       <  2:499690/140‑1 (MQ=255)

                                                                                                                            ggAACGATAAGAAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGTGGCTGGCGCAGGATGATTTCTCCGGTGAGGTGCCGTATCAGGCCGATTGCGTGa      >  2:615592/1‑140 (MQ=255)

                                                                                                                            ggAACGATAAGAAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGTGGCTGGCGCAGGATGATTTCTCCGGTGAGGTGCCGTATCAGGCCGATTGCGTGa      >  1:837395/1‑140 (MQ=255)

                                                                                                                            ggAACGATAAGAAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGTGGCTGGCGCAGGATGATTTCTCCGGTGAGGTGCCGTATCAGGCCGATTGCGTGa      >  1:60839/1‑140 (MQ=255)

                                                                                                                                cGATAAGAAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGTGGCTGGCGCAGGATGATTTCTCCGGTGAGGTGCCGTATCAGGCCGATTGCGTGATCCt  >  1:5126/1‑140 (MQ=255)

AATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTATTCTTAAGGGAACGATAAGGAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGTGGCTGGCGCAGGATGATTTCTCCGGTGAGGTGCCGTATCAGGCCGATTGCGTGATCCT  >  NC_000913/1487092‑1487359

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `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