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
A11 F20 I0 R1	35	38.1	1546666	86.7%	1340959	142.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	1,764,427	G→A	12.4%	intergenic (‑41/+286)	sufA ← / ← rydB	iron‑sulfur cluster insertion protein SufA/small regulatory RNA RydB

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,764,427	0	G	A	12.4%	85.6 / 5.5	41	intergenic (‑41/+286)	sufA/rydB	iron‑sulfur cluster insertion protein SufA/small regulatory RNA RydB
Reads supporting (aligned to +/- strand): ref base G (22/13); new base A (3/2); total (26/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.61e-01

TTTGCCACCAGCTCACGGATGTGTATCGCCGCTGCGGGTGTCAGCGTTAAGCCTTGCCAGGCGAAATCTTGTGGGTTAAAGGTTCCTGAATGCATGTCCATCGATTTACCTCACTTCATCGCTTTCAGCGTATAACAGCATGTTAGTGATAATGATTATCAGTTCAACCCAGCAAACGCAGGGGCTTTACCGTAAAACATGCTTTTTGCCTGCTTTTAATAAGCATAGACCCTGATGTGTGGGTTAACAGGCACGCTAAGAATTAGGTATCTCATTGT  >  NC_000913/1764286‑1764563

tttGCCACCAGCTCACGGATGTGTATCGCCGCGGCGGGTGTCAGCGGTAAGCCTTGCCAGGCGAAATCTTGTGGGTTAAAGGTTCCTGAATGCATGTCCATCGATTTACCTCACTTCATCGCTTTCAGCGTATAACAGCATGt                                                                                                                                         <  1:346593/143‑1 (MQ=255)

     cgccaGCTCAGGGATGTGGGTCGTCGCTGCGTGTGTCATCGTTAAGCCTTGCCTGGCGAAATCTTGTGGGTTAAAGGTTCCTGAATGCATGTCCATCGATTTATCTCACTTCATCGCTTTCAGCGTATAACAGCATATTAGTg                                                                                                                                    <  2:626280/141‑1 (MQ=255)

       ccaGCTCACGGATGTGTATCGCCGCAGCGGGTGTCAGCGTTAAGCCTTGCCAGGCGAAAGCTGGGGGGGTAAAGCGTCCTGAATGCCAGTCCACCGATTTACCCCACCCCATCGCTGTCAGCGTACAACAGCAGGTTCGCGAt                                                                                                                                  >  2:480107/1‑143 (MQ=255)

                         tCGCCGCTGCGGGTGTCAGCGTTAAGCCTTGCCAGGCGAAATCTTGTGGGTTAAAGGTTCCTGAATGCATGTCCATCGATTTACCTCACTTCATCGCTTTCCGCGTATAACAGCATGTTAGTGATAATGATTATCAGTTCAAc                                                                                                                >  1:157362/1‑143 (MQ=255)

                          cgccgcTGCGGGGGTCAGCGTTAAGCCTTACCAGCCGAAATCTTGTGGCTTAACGGATACTGGATGCATGTCCATCGATTTACCTCACTTCATCGCTTTCAGCGTATAACAGCATATTAGCGATAATGATTATCAGTTCAAcc                                                                                                               >  2:227652/1‑143 (MQ=255)

                           gccgcTGCGGGTGTCAGCGTTAAGCCTTGCCAGGCGAAATCTTGTGGGTTAAAGGTTCCTGAATGCATGTCCATCGATTTACCTCACTTCATCGCTTTCAGCGTATACCAGCATGTTAGTGATCATGATTATCAGTTCAAccc                                                                                                              >  1:653285/1‑143 (MQ=255)

                                    ggTGTCAGCGTTAAGCCTTGCCAGGCGAAATCTTGTGGGTTAAAGGTTCCTGAATGCATGTCCATCGATTTACCTCACTTCATCGCTTTCAGCGTATAACAGCATGTTAGTGATAATGATTATCAGTTCAACCCAGCAAACGc                                                                                                     >  2:349653/1‑143 (MQ=255)

                                          aGCGTTAAGCCTTGCCAGGCGAAATCTTGTGGGTTAAAGGTTCCTGAATGCATGTCCATCGATTTACCTCACTTCATCGCTTTCAGCGTATAACAGCATGTTAGTGATAATGATTATCAGTTCAACCCAGCAAACGCAGGGGc                                                                                               >  1:327342/1‑143 (MQ=255)

                                                         cAGGCGAAATCTTGTGGGTTAAAGGTTCCTGAATGCATGTCCATCGATTTACCTCACTTCATCGCTTTCAGCGTATAACAGCATGTTAGTGATAATGATTATCAGTTCAACCCAGCAAACGCAGGGGCTTTACCGTAAAACAt                                                                                >  1:360924/1‑143 (MQ=255)

                                                          agcctaaaTCTTGTGGGTTATTGGTTCCCAAAAGCATGTTCATCGTTCTACCTCACGTCATCGCTTTCAGCGTATAACAGCATGTTAGTGATAATGATTATCAGTTCAACCCAGCAAACGCAGGGGCTTTACCGTAAAACATg                                                                               <  1:102621/138‑1 (MQ=255)

                                                             cGAAATCTTGTGGGTTAAAGGTTCCTGAATGCATGTCCATCGATTTACCTCACTTCATCGCTTTCAGCGTATAACAGCATGTTAGTGATAATGATTATCAGTTCAACCCAGCAAACGCAGGGGCTTTACCGTAAAACATGCtt                                                                            >  2:419539/1‑143 (MQ=255)

                                                                aaTCTTGTGGGTTAAAGGTTCCTGAATGCATGTCCATCGATTTACCTCACTTCATCGCTTTCAGCGTATAACAGCATGCCAGTGCTTATGAGTATCAGTTCAACCCAGCAAACGCAGGGGCTTTACCGTAAAACATGCttttt                                                                         <  2:159816/143‑1 (MQ=255)

                                                                  tCTTGTGGGTTAAAGGTTCCTGAATGCATGTCCATCGATTTACCTCACTTCATCGCTTTCAGCGTATAACAGCATGTTAGTGATAATGATTATCAGTTCAACCCAGCAAACGAAAGGACTTTACCGTAAAAGAAGCATTATGc                                                                       >  1:678106/1‑143 (MQ=255)

                                                                        gggTTAAAGGTTCCTGAATGCATGTCCATCGATTTACCTCACTTCATCGTTTTCAGCGTATAACAGCATGTTAGTGATAATGATTATCAGTTCAACCCAGCAAACGCAGGGGCTTTACCGTAAAACATGCTTTTTGCCTGCtt                                                                 <  1:373690/143‑1 (MQ=255)

                                                                         ggTTAAAGGTTCCTGAATGCATGTCCATCGATTTACCACACTTCATCGCTTTCAGCGTATAACAGCATGTTAGTGATAATGATTATCAGTTCAACCCAGCAAACGCAGGGGCTTTACCGTAAAACATGCTTTTTGCCTGCttt                                                                <  1:269650/143‑1 (MQ=255)

                                                                          gTTAAAGGTTCCTGAATGCATGTCCATCGATTTACCTCACTTCATCGCTTTCAGCGTATAACAGCATTTTAGTGATAATGATTATCAGTTCAACCCACCAAACGCAGGGGCTTTCCCGTAAAACATGCTTTTTACCTCCtttt                                                               >  2:117077/1‑143 (MQ=255)

                                                                          gTTAAAGGTTCCTGAATGCATGTCCATCGATTTACCTCACTTCATCGCTTTCAGCGTATAACAGCATGTTAGTGATAATGATTATCAGTTCAACCCAGCAAACGCAGGGGCTTTACCGTCAAACATGCTTTTTTCCTGCtttt                                                               >  1:552701/1‑143 (MQ=255)

                                                                               aGGTACCTGAATGCATGTCCATCGATTTACCTCACTTCAGCGCTTTCAGCGTATAACAGCATATTAGTGATAATGATTATCAGTTCAACCCAGCAAACGCAGGGGCTTTACCGTAAAACATGCTTTTTGCCTGCTTTtaataa                                                          <  1:173470/143‑1 (MQ=255)

                                                                                   gccTGTATGCATGTCCATCGATTTACCTCACTTCATCGCTTTCAGCGTATAACAGCATGTTAGTGATACTGGATAATAGTTCCACCTTCTATTCTCTGGGGCTTTACCGTAAAACATGCTTTTTGCCTGCTTTTAATAAGCAt                                                      <  2:670575/142‑1 (MQ=255)

                                                                                     cTGAATGCATGTCCATCGATTTACCTCACTTCATCGCTTTCAGCGTATAACAGCATGTTAGTGATAATGATTATCAGTTCAACCCAGCAAACGCAGGGGCTTTACCGTAAAACATGCTTTTTGCCTGCTTTTAATAAGCATAg                                                    >  1:176728/1‑143 (MQ=255)

                                                                                      tGAATGCATGTCCATCGATTTACCTCACTTCATCGCTTTCAGCGTATAACAGCATGTTAGTGATAATGATTATCAGTTCAACCCAGCAAACGCAGGGGCTTTACCGTAAAACATGCTTTTTGCCTGCTTTTAATAAGCATAGa                                                   >  1:614956/1‑143 (MQ=255)

                                                                                      tGAATGCATGTCCATCGATTTACCTCACTTCATCGCTTTCAGCGTATAACAGCATGTTAGTGATAATGATTATCAGTTCAACCCAGCAAACGCAGGGGCTTTACCGTAAAACATGCTTTTTGCCTGCTTTTAATAAGCATAGa                                                   <  1:592208/143‑1 (MQ=255)

                                                                                          tGCATGTCCATCGATTTACCTCACTTCATCGCTTTCAGCGTATAACAGCATATTAGTGATAATGATTATCAGTTCAACCCAGCAAACGCAGGGGCTTTACCGTAAAACATGCTTTTTGCCTGCTTTTAATAAGCATAGACCCt                                               >  1:86828/1‑143 (MQ=255)

                                                                                            cATGTCCATCGATTTACCTCACTTCATAGCTTTCAGCCTAGAACAGCATGTTAGTGATAATGATTATCAGTTCAACCCAGCAAACGCAGAGGCTTTACCGTAAAACATGCTTTTTGCCTGCTTTTAATAAGCATAGACCATGa                                             >  2:267764/1‑143 (MQ=255)

                                                                                             aTGTCCATCGATTTACCTCACTTCATCGCTTTCAGCGTATAACAGCATGTTAGTGATAATGATTATCAGTTCAACCCAGCAAACGCAGGGGCTTTACCGTAAAACATGCTTTTTGCCTGCTGTTAATAAGCATAGAACCTGAt                                            >  2:271824/1‑143 (MQ=255)

                                                                                              tGTCCATCGATTTACCTCACTTCATCGCTTTCAGCGTATAACAGCATGTTAGTGATCATGATTATCAGTTCAACCCAGCAAACGCAGGGGCTTTACCGTAAAACATGCTTTTTGCCTGCTTTTAATAAGCATAGACCCTGAtg                                           >  2:621600/1‑143 (MQ=255)

                                                                                               gTCCATCGATTTACCTCACTTCATCGCTTTCAGCGTATAAGAGCATGATAGTGATAATGATTATCAGGTCACCCCAGCAAACGCAGGGGCTTTACCGTAAAACATGCTTTTTGCCTCCCTTTAATAAGCATAGCCCCTCAtgc                                          >  1:736395/1‑142 (MQ=255)

                                                                                               gTCCATCGATTTACCTCACTTCATCGCTTTCAGCGTATAACAGCATGTTAGTGATAATGATTATCAGTTCAACCCAGCAAACGCAGGGGCTTTACCGTAAAACATGCTTTTTGCCTGCTTTTAATAAGCATAGACCCTGAtgt                                          >  2:137611/1‑143 (MQ=255)

                                                                                                     cgctttACCTCATTTCATCGCTTTCAGCGTATAACAGCATGTTAGTGATAATGATTATCAGTTCAACCCAGCAAACGCAGGGGCTTTACCGTAAAACATGCTTTTTGCCTGCTTTTAATATGCATAGACCCTGATGTGTGGGt                                    <  2:550518/140‑1 (MQ=255)

                                                                                                     cGATTTACCTCACTTCATCGCTTTCAGCGTATAACAGCATGTTAGTGATAATGATTATCAGTTCAACCCAGCAAACGCAGGGGCTTTACCGTAAAACATGCTTTTTGCCTGCTTTTAATAAGCATAGACTCTGATGTGTGGGt                                    >  1:698829/1‑143 (MQ=255)

                                                                                                     cGATTTACCTCACTTCATCGCTTTCAGCGTATAACAGCATGTTAGTGATAATGATTATCAGTTCAACCCAGCAAACGCAGGGGCTTTACCGTAAAACATGCTTTTTGCCTGCTTTTAATAACCATCGACCCTGATGTGTGGGt                                    >  1:415077/1‑143 (MQ=255)

                                                                                                      gATTTACCTCACTTCATCGCTTTCAGTGTATAACAGCATGTTAGTGATAATGATTATCAGTTTATTTTATCATACGTAGGGGCTTTACCGTAAAACATGCTTGTTGCCTGCTTTTAATAAGCATAGACCCTGATGTGTGGGtt                                   <  1:593241/143‑1 (MQ=255)

                                                                                                        tttACCTCACTTCATCGCTTTTAGCGTTTAACAGTATGTTAGTGATAATGATTATCAGTTCAACCCAGCAAACGCAGGGGCTTTACCGTAAAACATGCTTTTTGCCTGCTTTTAATAAGCATAGACCCTGATGTGTGGGTTaa                                 <  1:593387/143‑1 (MQ=255)

                                                                                                            cgtCACGTCATCGCTTTCAGCGTATAACGGCAGGTTAGTGATAATGATGATCAGGTCGACCCAGCAAACGCAGGGGCTTTACCGTAAAACATGCTTTTTGCCTGCTTTTAATAAGCATAGACCCTGATGTGTGGGTTAACAgg                             <  2:187554/141‑1 (MQ=255)

                                                                                                             cTCACTTCATCGCTTTCAGCGTATAACAGCATGTTAGTGATAATGATTATCAGTTCAACCCAGCAAACGCAGGGGCTTTACCGTAAAACCTGCTTTTTGCCTGCTTTTAATAAGCATAGACCCTGATGTGTGGGTTAACAGGc                            >  1:674085/1‑143 (MQ=255)

                                                                                                             cTCACTTCATCGCTTTCAGCGTATAACAGCATATTAGTGATAATGATTATCAGTTCAACCCAGCAAACGCAGGGGCTTTACCGTAAAACATGCTTTTTGCCTGCTTTTAATAAGCATAGACCCTGATGTGTGGCTTAACAGGc                            >  2:126682/1‑143 (MQ=255)

                                                                                                                    cATCGCTTTCTTCGTATAACAGCTTGTTAGTGATAATGAGTATCAGTTCAACCCAGCTAACGTAGGGGCTTTACTTGAAAACATGCTTTTTGCCTGCTTTTAATACGCATAGACCCTGATGTGTGGGTTAACAGGCACGCTaa                     <  2:156370/143‑1 (MQ=255)

                                                                                                                    cATCGCTTTCAGCGTATAACAGCATGTTAGTGATAATGATTATCAGTTCAACCCAGCAAACGCAGGCGCTTTACCGTAAAACATGCTTTTTGCATGCTAATAATAAGCATAAACAAAGATATGTGGGTTAACAGGCAACCTaa                     >  1:29689/1‑143 (MQ=255)

                                                                                                                     aTCGCTTTCAGCGTATAACAGCATGTGAGTGATAATGATTATCAGTTCAACCCAGCAAACGCAGGGGCTTTACCGTAAAACATGCTTTTTGCCTGCTTTTAATGAGCATAGACCCTGAAGTGTGGGTTGACCGGCCAGCTAAg                    >  2:674421/1‑143 (MQ=255)

                                                                                                                                    taAAAGCGTGTTAGGGAGAATGATTATCAGTTCAACCCAGCAAACGCAGGGGCGTTACCGTAAAACATGCTTTTTGCCTGCTTTTAATAAGCATAGACCCTGATGTGTGGGTTAACAGGCACGCTAAGAATTAGGTATCTCAt     <  2:512795/143‑1 (MQ=255)

                                                                                                                                       cAGCATGTTAGTGATAATGATTATCAGTTCAACCCAGCAAACGCAGGGGCTTTACCGTAAAACATGCTTTTTTCCTGCTTTTAATAAGCATAGACCCTGATGTGTGGGTTAACAGTCACGCTAAGAATTAGGTATCTCATTGt  >  1:339083/1‑143 (MQ=255)

TTTGCCACCAGCTCACGGATGTGTATCGCCGCTGCGGGTGTCAGCGTTAAGCCTTGCCAGGCGAAATCTTGTGGGTTAAAGGTTCCTGAATGCATGTCCATCGATTTACCTCACTTCATCGCTTTCAGCGTATAACAGCATGTTAGTGATAATGATTATCAGTTCAACCCAGCAAACGCAGGGGCTTTACCGTAAAACATGCTTTTTGCCTGCTTTTAATAAGCATAGACCCTGATGTGTGGGTTAACAGGCACGCTAAGAATTAGGTATCTCATTGT  >  NC_000913/1764286‑1764563

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A