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
A2 F28 I1 R1	155	60.3	2039550	99.3%	2025273	138.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,635,059	C→T	S263S (TCG→TCA)	ydfN ←	Qin prophage; putative side tail fiber assembly protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,635,059	0	C	T	98.2%	138.4 / ‑4.2	54	S263S (TCG→TCA)	ydfN	Qin prophage; putative side tail fiber assembly protein
Reads supporting (aligned to +/- strand): ref base C (0/1); new base T (25/28); total (25/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.97e-01

CGGTGATGGTGTGTCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACA‑‑GTATGTGCATGCGCGCCTGCGCTTGCAGCAGTGCCGGACAGCGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATCGCGGTATAACCATTAGGGAAAATGCTCGTGT  >  NC_000913/1634956‑1635189

cGGTGATGGTGTGTCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACA‑‑GTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCt                                                                                                >  2:769956/1‑140 (MQ=11)

 ggTGATGGTGTGTCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACA‑‑GTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTg                                                                                               <  2:295899/140‑1 (MQ=11)

    gATGGTGTGTCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACA‑‑GTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCAt                                                                                            >  2:818618/1‑140 (MQ=11)

    gATGGTGTGTCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACA‑‑GTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCAt                                                                                            >  2:600061/1‑140 (MQ=11)

           tgtCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACA‑‑GTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGt                                                                                     <  2:400478/140‑1 (MQ=14)

           tgtCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACA‑‑GTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGt                                                                                     <  1:708586/140‑1 (MQ=14)

           tgtCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACA‑‑GTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGt                                                                                     <  1:704639/140‑1 (MQ=14)

             tCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACA‑‑GTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCt                                                                                   >  2:11384/1‑140 (MQ=14)

                 tgtgAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACA‑‑GTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGc                                                                                <  1:521783/140‑1 (MQ=14)

                   tgAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACA‑‑GTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTc                                                                                    >  2:358369/1‑133 (MQ=14)

                   tgAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACA‑‑GTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTc                                                                                    <  1:358369/133‑1 (MQ=14)

                   tgAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACA‑‑GTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCAc                                                                             >  2:717774/1‑140 (MQ=17)

                    gAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACA‑‑GTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACt                                                                            <  1:11384/140‑1 (MQ=17)

                     aaCCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTg                                                                                  >  2:961606/1‑135 (MQ=14)

                     aaCCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTg                                                                                  <  1:961606/135‑1 (MQ=14)

                     aaCCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACA‑‑GTATGCGCGTGTGCACCTGCGATTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTa                                                                           >  1:989549/1‑140 (MQ=17)

                       ccAATCGCAACGGAGTGCGTATGAGCACCAATACCGACA‑‑GTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACt                                                                            >  1:516998/1‑137 (MQ=17)

                       ccAATCGCAACGGAGTGCGTATGAGCACCAATACCGACA‑‑GTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACt                                                                            <  2:516998/137‑1 (MQ=17)

                       ccAATCGCAACGGAGTGCGTATGAGCACCAATACCGACA‑‑GTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTAcc                                                                         >  2:68662/1‑140 (MQ=17)

                         aaTCGCAACGGAGTGCGTATGAGCACCAATACCGACA‑‑GTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGc                                                                       >  1:162634/1‑140 (MQ=17)

                          aTCGCAACGGAGTGCGTATGAGCACCAATACCGACA‑‑GTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGt                                                                                     <  2:662448/125‑1 (MQ=14)

                          aTCGCAACGGAGTGCGTATGAGCACCAATACCGACA‑‑GTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGt                                                                                     >  1:662448/1‑125 (MQ=14)

                               aaCGGAGTGCGTATGAGCACCAATACCGACA‑‑GTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCttgttg                                                                 <  1:543662/140‑1 (MQ=18)

                                 cGGAGTGCGTATGAGCACCAATACCGACA‑‑GTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTtgtg                                                               <  1:717774/140‑1 (MQ=18)

                                              aGCACCAATACCGACA‑‑GTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCGTTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCcg                                                  >  1:470069/1‑140 (MQ=21)

                                              aGCACCAATACCGACA‑‑GTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCcg                                                  >  1:17751/1‑140 (MQ=21)

                                                  ccAATACCGACA‑‑GTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCt                                              >  2:547129/1‑140 (MQ=25)

                                                   cAATACCGACA‑‑GTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCtt                                             >  2:192916/1‑140 (MQ=25)

                                                          gACA‑‑GTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCgcgc                                               <  2:313785/131‑1 (MQ=25)

                                                          gACA‑‑GTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCgcgc                                               >  1:313785/1‑131 (MQ=21)

                                                                gTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAAt                                  <  1:145798/140‑1 (MQ=37)

                                                                 tATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATc                                 <  1:192916/140‑1 (MQ=37)

                                                                 tATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATc                                 >  1:436117/1‑140 (MQ=37)

                                                                  aTGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATcg                                <  1:847910/140‑1 (MQ=37)

                                                                  aTGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATcg                                <  2:17751/140‑1 (MQ=37)

                                                                  aTGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATcg                                <  1:818618/140‑1 (MQ=37)

                                                                  aTGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATcg                                <  1:592490/140‑1 (MQ=37)

                                                                        gtgtgcaccTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATCGCGGtat                          <  1:799746/133‑1 (MQ=255)

                                                                        gtgtgcaccTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATCGCGGtat                          <  1:769956/133‑1 (MQ=255)

                                                                        aTGCGCGCCTGCGCTTGCAGCAGTGCCGGACAGCGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATCGCGGtat                          <  1:1001846/140‑1 (MQ=255)

                                                                           tgcaccTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATcg                                >  2:566626/5‑131 (MQ=255)

                                                                           tgcaccTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATcg                                >  2:61214/5‑131 (MQ=255)

                                                                           tgcaccTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATcg                                <  1:61214/127‑1 (MQ=255)

                                                                           tgcaccTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATcg                                <  1:566626/127‑1 (MQ=255)

                                                                           tgcaccTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATCGCGGTATAAc                       >  1:446038/5‑140 (MQ=255)

                                                                           tgcaccTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATCGCGGTATAAc                       >  1:156673/5‑140 (MQ=255)

                                                                           tgcaccTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAACACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCACAATCCCCGCGCTTAGATTTGAAATCGCGGTATAAc                       >  2:381589/5‑140 (MQ=255)

                                                                             caccTGCGCTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATCGCGGTATAACCa                     <  1:879349/138‑1 (MQ=255)

                                                                                     cTTGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATCGCGGTATAACCATTAGGGaa             >  2:111525/1‑140 (MQ=255)

                                                                                      ttGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCGTTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATCGCGGTATAACCATTAGGGaaa            <  2:470069/140‑1 (MQ=255)

                                                                                      ttGCAGCAGTGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTGCCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATCGCGGTATAACCATTAGGGaaa            <  2:156673/140‑1 (MQ=255)

                                                                                            cagTGCCGGACAGTGAGT‑GGGTATGAACACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCACAATCCCCGCGCTTAGATTTGAAATCGCGGTATAACCATTAGGGAAAATGCTc      <  1:381589/140‑1 (MQ=255)

                                                                                               tGCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATCGCGGTATAACCATTAGGGAAAATGCTCgtg   >  2:796338/1‑140 (MQ=255)

                                                                                                gCCGGACAGTGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATCGCGGTATAACCATTAGGGAAAATGCTCgtgt  <  1:796338/140‑1 (MQ=255)

CGGTGATGGTGTGTCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACA‑‑GTATGTGCATGCGCGCCTGCGCTTGCAGCAGTGCCGGACAGCGAGT‑GGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATCGCGGTATAACCATTAGGGAAAATGCTCGTGT  >  NC_000913/1634956‑1635189

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 22 ≤` `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