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 F169 I1 R1	62	44.4	970160	98.1%	951726	147.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	1,125,066	G→C	E729Q (GAG→CAG)	cfiB_1 →	2‑oxoglutarate carboxylase small subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,125,066	0	G	C	100.0%	150.1 / NA	39	E729Q (GAG→CAG)	cfiB_1	2‑oxoglutarate carboxylase small subunit
Reads supporting (aligned to +/- strand): ref base G (0/0); new base C (25/14); total (25/14)

TCCTGAGCGATCAAACATTTATACTTTAGAGTATTATGTCAAACTAGCTAAAGAGTTAGAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTGAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATGGTTTATTAACATACAAACAAGCAATAGATGCTGGTGTCGATATCATTGATACTGCTGTTGCTTCAATGAGTGGTTTAACAA  >  USA300TCH1516_ALE/1124927‑1125207

tCCTGAGCGATCAAACATTTATACTTTAGAGTATTATGTCAAACTAGCTAAAGAGTTAGAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTaaaa                                                                                                                                       >  4:342114/1‑148 (MQ=255)

        gATCAAACATTTATACTTTAGAGTATTATGTCAAACTAGCTAAAGAGTTAGAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGt                                                                                                                               >  4:172918/1‑148 (MQ=255)

                      aCTTTAGAGTATTATGTCAAACTAGCTAAAGAGTTAGAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTa                                                                                                                        <  1:51615/141‑1 (MQ=255)

                            gagTATTATGTCAAACTAGCTAANGAGTTAGAACGTNAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTc                                                                                                           >  3:399993/1‑148 (MQ=255)

                            gagTATTATGTCAAACTAGCTAAAGAGTTAGAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTc                                                                                                           >  4:274834/1‑148 (MQ=255)

                            gagTATTATGTCAAACTAGCTAAAGAGTTAGAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTc                                                                                                           >  3:352851/1‑148 (MQ=255)

                                    tGTCAAACTAGCTAAAGAGTTAGAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTca                                                                                                          >  1:31949/1‑141 (MQ=255)

                                        aaaCTAGCTAAAGAGTTAGAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATa                                                                                               >  3:21479/1‑148 (MQ=255)

                                              gCTAAAGAGTTAGAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGAt                                                                                                <  2:58044/141‑1 (MQ=255)

                                              gCTAAAGAGTTAGAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTg                                                                                         <  4:298190/148‑1 (MQ=255)

                                              gCTAAAGAGTTAGAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTg                                                                                         <  4:160479/148‑1 (MQ=255)

                                                  aaGAGTTAGAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTaa                                                                                     >  3:253682/1‑148 (MQ=255)

                                                  aaGAGTTAGAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTaa                                                                                     >  3:253962/1‑148 (MQ=255)

                                                     agTTAGAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATgg                                                                                  >  3:83440/1‑148 (MQ=255)

                                                       ttAGAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATGGtt                                                                                <  3:309120/148‑1 (MQ=255)

                                                       ttAGAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATGGtt                                                                                <  3:353991/148‑1 (MQ=255)

                                                        tAGAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATGGttt                                                                               <  3:11118/148‑1 (MQ=255)

                                                             cGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATGGTTTATTaa                                                                          <  4:306165/148‑1 (MQ=255)

                                                                                     aTTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATGGTTTATTAACATACAAACAAGCAATAGATGCTg                                                  <  3:182093/148‑1 (MQ=255)

                                                                                             tatGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATGGTTTATTAACATACAAACAAGCAATAGATGCTGGTGTCGat                                          <  3:76308/148‑1 (MQ=255)

                                                                                                 gCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATGGTTTATTAACATACAAACAAGCAATAGATGCTGGTGTCGATATCa                                      >  4:374566/1‑148 (MQ=255)

                                                                                                 gCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATGGTTTATTAACATACAAACAAGCAATAGATGCTGGTGTCGATATCa                                      >  4:305875/1‑148 (MQ=255)

                                                                                                 gCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATGGTTTATTAACATACAAACAAGCAATAGATGCTGGTGTCGATATCa                                      >  4:214405/1‑148 (MQ=255)

                                                                                                   aGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATGGTTTATTAACATACAAACAAGCAATAGATGCTGGTGTCGATATCAtt                                    >  3:385718/1‑148 (MQ=255)

                                                                                                   aGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATGGTTTATTAACATACAAACAAGCAATAGATGCTGGTGTCGATATCAtt                                    >  3:241839/1‑148 (MQ=255)

                                                                                                        tattaAAACCTAAAGCCGCTTAGGAATTGAGGGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATGGTTTATTAACATACAAACAAGCAATAGATGCTGGTGTCGATATCa                                      >  2:11622/1‑141 (MQ=255)

                                                                                                        tattaAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATGGTTTATTAACATACAAACAAGCAATAGATGCTGGTGTCGATATCa                                      >  2:58266/1‑141 (MQ=255)

                                                                                                        tattaAAACCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATGGTTTATTAACATACAAACAAGCAATAGATGCTGGTGTCGATATCATTGATAc                               >  4:378641/1‑148 (MQ=255)

                                                                                                              aaCCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAGTCAGCTGTAGATTTACCAATTCATCTGCACACTCATGATACAAGTGGTAATGGTTTATTAACATACAAACAAGCAATAGATGCTGGTGTCGATATCATTGATACTGCTGt                         >  4:145312/1‑148 (MQ=255)

                                                                                                              aaCCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCGCACTCATGATACAAGTGGTAATGGTTTATTAACATACAAACAAGCAATAGACGCTGGTGTCGATCTCATTGAAActacggt                         >  4:163009/1‑143 (MQ=255)

                                                                                                               aCCTAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATGGTTTATTAACATACAAACAAGCAATAGATGCTGGTGTCGATATCATTGATACTGCTGtt                        <  4:379576/148‑1 (MQ=255)

                                                                                                                  tAAAGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATGGTTTATTAACATACAAACAAGCAATAGATGCTGGTGTCGATATCATTGATACTGCTGTTGCt                     >  3:68436/1‑148 (MQ=255)

                                                                                                                    aaGCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATGGTTTATTAACATACAAACAAGCAATAGATGCTGGTGTCGATATCATTGATACTGCTGTTGCTTc                   >  3:190250/1‑148 (MQ=255)

                                                                                                                      gCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATGGTTTATTAACATACAAACAAGCAATAGATGCTGGTGTCGATATCATTGATACTGCTGTTGCTTCaa                 >  3:372096/1‑148 (MQ=255)

                                                                                                                      gCCGCTTACGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATGGTTTATTAACATACAAACAAGCAATAGATGCTGGTGTCGATATCATTGATACTGCTGTTGCTTCaa                 >  3:386872/1‑148 (MQ=255)

                                                                                                                              cGAATTGATTGGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATGGTTTATTAACATACAAACAAGCAATAGATGCTGGTGTCGATATCATTGATACTGCTGTTGCTTCAATGAGTGGt         <  4:253962/148‑1 (MQ=255)

                                                                                                                                  ttgattgGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATGGTTTATTAACATACAAACAAGCAATAGATGCTGGTGTCGATATCATTGATACTGCTGTTGCTTCAATGAGTGGTTTaa     >  3:147029/1‑148 (MQ=255)

                                                                                                                                     attgGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATGGTTTATTAACATACAAACAAGCAATAGATGCTGGTGTCGATATCATTGATACTGCTGTTGCTTCAATGAGTGGTTTAACaa  <  4:361166/148‑1 (MQ=255)

                                                                                                                                     attgGTCAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATGGTTTATTAACATACAAACAAGCAATAGATGCTGGTGTCGATATCATTGATACTGCTGTTGCTTCAATGAGTGGTTTAACaa  <  4:369394/148‑1 (MQ=255)

TCCTGAGCGATCAAACATTTATACTTTAGAGTATTATGTCAAACTAGCTAAAGAGTTAGAACGTGAAGGTTTCCATATTTTAGCGATTAAAGATATGGCAGGCTTATTAAAACCTAAAGCCGCTTACGAATTGATTGGTGAGTTAAAATCAGCTGTAGATTTACCAATTCATCTTCACACTCATGATACAAGTGGTAATGGTTTATTAACATACAAACAAGCAATAGATGCTGGTGTCGATATCATTGATACTGCTGTTGCTTCAATGAGTGGTTTAACAA  >  USA300TCH1516_ALE/1124927‑1125207

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A