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 F28 I1 R1	161	75.5	2581324	99.3%	2563254	138.8

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,017,729	A→G	K392K (AAA→AAG)	fliI →	flagellum‑specific ATP synthase FliI

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,017,729	0	A	G	98.0%	172.8 / ‑6.0	49	K392K (AAA→AAG)	fliI	flagellum‑specific ATP synthase FliI
Reads supporting (aligned to +/- strand): ref base A (0/1); new base G (26/22); total (26/23)
Fisher's exact test for biased strand distribution p-value = 4.69e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACGGTCACATTGTGCTGTCTCGCCGACTGGCGGAAGCCGGGCACTATCCGGCTATCGATATTGAAGCGTCGATCAGCCGCGCAATGACGGCGTTGATCAGTGAGCAACATTACGCGCGAGTGCGCACCTTCAAACAGCTGTTGTCGAGTTTTCAGCGTAACCGCGATCTGGTTAGCGTCGGCGCGTATGCCAAAGGCAGCGATCCGATGCTCGATAAAGCCATCGCCCTGTGGCCGCAGCTGGAGGGCTATTTGCAACAAGGCATTT  >  NC_000913/2017596‑2017862

aCGGTCACATTGTGCTGTCTCGCCGACTGGCGGAAGCCGGGCACTATCCGGCTATCGATATTGAAGCGTCGATCAGCCGCGCAATGACGGCGTTGATCAGTGAGCAACATTACGCGCGAGTGCGCACCTTCAAGCAGCtg                                                                                                                                 >  1:1057644/1‑140 (MQ=255)

aCGGTCACATTGTGCTGTCTCGCCGACTGGCGGAAGCCGGGCACTATCCGGCTATCGATATTGAAGCGTCGATCAGCCGCGCAATGACGGCGTTGATCAGTGAGCAACATTACGCGCGAGTGCGCACCTTCAAGCAGCtg                                                                                                                                 <  1:1085220/140‑1 (MQ=255)

aCGGTCACATTGTGCTGTCTCGCCGACTGGCGGAAGCCGGGCACTATCCGGCTATCGATATTGAAGCGTCGATCAGCCGCGCAATGACGGCGTTGATCAGTGAGCAACATTACGCGCGAGTGCGCACCTTCAAGCAGCtg                                                                                                                                 <  2:949500/140‑1 (MQ=255)

    tCACATTGTGCTGTCTCGCCGACTGGCGGAAGCCGGGCACTATCCGGCTATCGATATTGAAGCGTCGATCAGCCGCGCAATGACGGCGTTGATCAGTGAGCAACATTACGCGCGAGTGCGCACCTTCAAGCAGCtgttgt                                                                                                                             >  1:929331/1‑140 (MQ=255)

    tCACATTGTGCTGTCTCGCCGACTGGCGGAAGCCGGGCACTATCCGGCTATCGATATTGAAGCGTCGATCAGCCGCGCAATGACGGCGTTGATCAGTGAGCAACATTACGCGCGAGTGCGCACCTTCAAGCAGCtgttgt                                                                                                                             >  1:1180317/1‑140 (MQ=255)

    tCACATTGTGCTGTCTCGCCGACTGGCGGAAGCCGGGCACTATCCGGCTATCGATATTGAAGCGTCGATCAGCCGCGCAATGACGGCGTTGATCAGTGAGCAACATTACGCGCGAGTGCGCACCTTCAAGCAGCtgttgt                                                                                                                             >  2:812407/1‑140 (MQ=255)

    tCACATTGTGCTGTCTCGCCGACTGGCGGAAGCCGGGCACTATCCGGCTATCGATATTGAAGCGTCGATCAGCCGCGCAATGACGGCGTTGATCAGTGAGCAACATTACGCGCGAGTGCACACCTTCAAGCAGCtgttgt                                                                                                                             >  1:188391/1‑140 (MQ=255)

    tCACATTGTGCTGTCTCGCCGACTGGCGGAAGCCGGGCACTATCCGGCTATCGATATTGAAGCGTCGATCAGCCGCGCAATGACGGCGTTGATCAGTGAGCAACATTACGCGCGAGGGCGCACCTTCAAGCAGCtgttgt                                                                                                                             >  1:1120442/1‑140 (MQ=255)

            tgCTGTCTCGCCGACTGGCGGAAGCCGGGCACTATCCGGCTATCGATATTGAAGCGTCGATCAGCCGCGCAATGACGGCGTTGATCAGTGAGCAACATTACGCGCGAGTGCGCACCTTCAAGCAGCTGTTGTCGAGtttt                                                                                                                     <  1:79183/140‑1 (MQ=255)

            tgCTGTCTCGCCGACTGGCGGAAGCCGGGCACTATCCGGCTATCGATATTGAAGCGTCGATCAGCCGCGCAATGACGGCGTTGATCAGTGAGCAACATTACGCGCGAGTGCGCACCTTCAAGCAGCTGTTGTCGAGtttt                                                                                                                     <  2:496/140‑1 (MQ=255)

              cTGTCTCGCCGACTGGCGGAAGCCGGGCACTATCCGGCTATCGATATTGAAGCGTCGATCAGCCGCGCAATGACGGCGTTGATCAGTGAGCAACATTACGCGCGAGTGTGCACCTTCAAGCAGCTGTTGTCGAGTTTTCa                                                                                                                   >  1:1151877/1‑140 (MQ=255)

               tGTCTCGCCGACTGGCGGAAGCCGGGCACTATCCGGCTATCGATATTGAAGCGTCGATCAGCCGCGCAATGACGGCGTTGATCAGTGAGCAACATTACGCGCGAGTGCGCACCTTCAAGCAGCTGTTGTCGAGTTTTCAg                                                                                                                  <  2:215843/140‑1 (MQ=255)

                      ccGACTGGCGGAAGCCGGGCACTATCCGGCTATCGATATTGAAGCGTCGATCAGCCGCGCAATGACGGCGTTGATCAGTGAGCAACATTACGCGCGAGTGCGCACCTTCAAGCAGCTGTTGTCGAGTTTTCAGCGTAAcc                                                                                                           <  2:1239801/140‑1 (MQ=255)

                      ccGACTGGCGGAAGCCGGGCACTATCCGGCTATCGATATTGAAGCGTCGATCAGCCGCGCAATGACGGCGTTGATCAGTGAGCAACATTACGCGCGAGTGCGCACCTTCAAGCAGCTGTTGTCGAGTTTTCAGCGTAAcc                                                                                                           <  2:305443/140‑1 (MQ=255)

                      ccGACTGGCGGAAGCCGGGCACTATCCGGCTATCGATATTGAAGCGTCGATCAGCCGCGCAATGACGGCGTTGATCAGTGAGCAACATTACGCGCGAGTGCGCACCTTCAAGCAGCTGTTGTCGAGTTTTCAGCGTAAcc                                                                                                           >  1:473686/1‑140 (MQ=255)

                      ccGACTGGCGGAAGCCGGGCACTATCCGGCTATCGATATTGAAGCGTCGATCAGCCGCGCAATGACGGCGTTGATCAGTGAGCAACATTACGCGCGAGTGCGCACCTTCAAGCAGCTGTTGTCGAGTTTTCAGCGTAAcc                                                                                                           <  1:1230364/140‑1 (MQ=255)

                        gACTGGCGGAAGCCGGGCACTATCCGGCTATCGATATTGAAGCGTCGATCAGCCGCGCAATGACGGCGTTGATCAGTGAGCAACATTACGCGCGAGTGCGCACCTTCAAGCAGCTGTTGTCGAGTTTTCAGCGTAACcgc                                                                                                         <  1:531625/140‑1 (MQ=255)

                          cTGGCGGAAGCCGGGCACTATCCGGCTATCGATATTGAAGCGTCGATCAGCCGCGCAATGACGGCGTTGATCAGTGAGCAACATTACGCGCGAGTGCGCACCTTCAAGCAGCTGTTGTCGAGTTTTCAGCGTAACCGCGa                                                                                                       <  2:1180317/140‑1 (MQ=255)

                           tGGCGGAAGCCGGGCACTATCCGGCTATCGATATTGAAGCGTCGATCAGCCGCGCAATGACGGCGTTGATCAGTGAGCAACATTACGCGCGAGTGCGCACCTTCAAGCAGCTGTTGTCGAGTTTTCAGCGTAACCGCGAt                                                                                                      <  2:1190873/140‑1 (MQ=255)

                           tGGCGGAAGCCGGGCACTATCCGGCTATCGATATTGAAGCGTCGATCAGCCGCGCAATGACGGCGTTGATCAGTGAGCAACATTACGCGCGAGTGCGCACCTTCAAGCAGCTGTTGTCGAGTTTTCAGCGTAACCGCGAt                                                                                                      >  1:993396/1‑140 (MQ=255)

                                       ggCACTATCCGGCTATCGATATTGAAGCGTCGATCAGCCGCGCAATGACGGCGTTGATCAGTGAGCAACATTACGCGCGAGTGCGCACCTTCAAGCAGCTGTTGTCGAGTTTTCAGCGTAACCGCGATCTGGTTAGCGTc                                                                                          >  1:571721/1‑140 (MQ=255)

                                             aTCCGGCTATCGATATTGAAGCGTCGATCAGCCGCGCAATGACGGCGTTGATCAGTGAGCAACATTACGCGCGAGTGCGCACCTTCAAGCAGCTGTTGTCGAGTTTTCAGCGTAACCGCGATCTGGTTAGCGTCGGcgcg                                                                                    <  2:993396/140‑1 (MQ=255)

                                                   cTATCGATATTGAAGCGTCGATCAGCCGCGCAATGACGGCGTTGATCAGTGAGCAACATTACGCGCGAGTGCGCACCTTCAAGCAGCTGTTGTCGAGTTTTCAGCGTAACCGCGATCTGGTTAGCGTCGGCGCGTATGcc                                                                              <  2:458435/140‑1 (MQ=255)

                                                      tCGATATTGAAGCGTCGATCAGCCGCGCAATGACGGCGTTGATCAGTGAGCAACATTACGCGCGAGTGCGCACCTTCAAGCAGCTGTTGTCGAGTTTTCAGCGTAACCGCGATCTGGTTAGCGTCGGcgcg                                                                                    <  2:518473/131‑1 (MQ=255)

                                                      tCGATATTGAAGCGTCGATCAGCCGCGCAATGACGGCGTTGATCAGTGAGCAACATTACGCGCGAGTGCGCACCTTCAAGCAGCTGTTGTCGAGTTTTCAGCGTAACCGCGATCTGGTTAGCGTCGGcgcg                                                                                    >  1:518473/1‑131 (MQ=255)

                                                             tGAAGCGTCGATCAGCCGCGCAATGACGGCGTTGATCAGTGAGCAACATTACGCGCGAGTGCGCACCTTCAAGCAGCTGTTGTCGAGTTTTCAGCGTAACCGCGATCTGGTTAGCGTCGGCGCGTATGCCAAAGGCAGCg                                                                    >  1:285310/1‑140 (MQ=255)

                                                                    tCGATCAGCCGCGCAATGACGGCGTTGATCAGTGAGCAACATTACGCGCGAGTGCGCACCTTCAAGCAGCTGTTGTCGAGTTTTCAGCGTAACCGCGATCTGGTTAGCGTCGGCGCGTATGCCAAAGGCAGCGATCCGAt                                                             >  2:327757/1‑140 (MQ=255)

                                                                    tCGATCAGCCGCGCAATGACGGCGTTGATCAGTGAGCAACATTACGCGCGAGTGCGCACCTTCAAGCAGCTGTTGTCGAGTTTTCAGCGTAACCGCGATCTGGTTAGCGTCGGCGCGTATGCCAAAGGCAGCGATCCGAt                                                             >  1:621824/1‑140 (MQ=255)

                                                                                gcAATGACGGCGTTGATCAGTGAGCAACATTACGCGCGAGTGCGCACCTTCAAGCAGCTGTTGTCGAGTTTTCAGCGTAACCGCGATCTGGTTAGCGTCGGCGCGTATGCCAAAGGCAGCGATCCGATGCTTGATAAAGc                                                 >  2:196603/1‑140 (MQ=255)

                                                                                 cAATGACGGCGTTGATCAGTGAGCAACATTACGCGCGAGTGCGCACCTTCAAGCAGCTGTTGTCGAGTTTTCAGCGTAACCGCGATCTGGTTAGCGTCGGCGCGTATGCCAAAGGCAGCGATCCGATGCTCGATAAAGcc                                                >  2:998472/1‑140 (MQ=255)

                                                                                     gACGGCGTTGATCAGTGAGCAACATTACGCGCGAGTGCGCACCTTCAAGCAGCTGTTGTCGAGTTTTCAGCGTAACCGCGATCTGGTTAGCGTCGGCGCGTATGCCAAAGGCAGCGATCCGATGCTCGATAAAGCCATCg                                            <  2:1101278/140‑1 (MQ=255)

                                                                                      aCGGCGTTGATCAGTGAGCAACATTACGCGCGAGTGCGCACCTTCAAGCAGCTGTTGTCGAGTTTTCAGCGTAACCGCGATCTGGTTAGCGTCGGCGCGTATGCCAAAGGCAGCGATCCGATGCTCGATAAAGCCATc                                             <  2:160286/138‑1 (MQ=255)

                                                                                      aCGGCGTTGATCAGTGAGCAACATTACGCGCGAGTGCGCACCTTCAAGCAGCTGTTGTCGAGTTTTCAGCGTAACCGCGATCTGGTTAGCGTCGGCGCGTATGCCAAAGGCAGCGATCCGATGCTCGATAAAGCCATc                                             >  1:160286/1‑138 (MQ=255)

                                                                                      aCGGCGTTGATCAGTGAGCAACATTACGCGCGAGTGCGCACCTTCAAGCAGCTGTTGTCGAGTTTTCAGCGTAACCGCGATCTGGTTAGCGTCGGCGCGTATGCCAAAGGCAGCGATCCGATGCTCGATAAAGCCATCGc                                           >  2:603496/1‑140 (MQ=255)

                                                                                                    tGAGCAACATTACGCGCGAGTGCGCACCTTCAAGCAGCTGTTGTCGAGTTTTCAGCGTAACCGCGATCTGGTTAGCGTCGGCGCGTATGCCAAAGGCAGCGATCCGATGCTCGATAAAGCCATCGCCCTGTGGCCGCAGc                             >  1:791955/1‑140 (MQ=255)

                                                                                                      aGCAACATTACGCGCGAGTGCGCACCTTCAAGCAGCTGTTGTCGAGTTTTCAGCGTAACCGCGATCTGGTTAGCGTCGGCGCGTATGCCAAAGCCAGCGATCCGATGCTCGATAAAGCCATCGCCCTGTGGCCGCAGCTg                           >  2:466926/1‑140 (MQ=255)

                                                                                                        cAACATTACGCGCGAGTGCGCACCTTCAAGCAGCTGTTGTCGAGTTTTCAGCGTAACCGCGATCTGGTTAGCGTCGGCGCGTATGCCAAAGGCAGCGATCCGATGCTCGATAAAGCCATCGCCCTGTGGCCGCAGCTGGa                         <  2:571721/140‑1 (MQ=255)

                                                                                                        cAACATTACGCGCGAGTGCACACCTTCAAGCAGCTGTTGTCGAGTTTTCAGCGTAACCGCGATCTGGTTAGCGTCGGCGCGTATGCCAAAGGCAGCGATCCGATGCTCGATAAAGCCATCGCCCTGTGGCCGCAGCTGGa                         <  2:188391/140‑1 (MQ=255)

                                                                                                         aaCATTACGCGCGAGTGCGCACCTTCAAGCAGCTGTTGTCGAGTTTTCAGCGTAACCGCGATCTGGTTAGCGTCGGCGCGTATGCCAAAGGCAGCGATCCGATGCTCGATAAAGCCATCGCCCTGTGGCCg                                 <  2:809182/131‑1 (MQ=255)

                                                                                                         aaCATTACGCGCGAGTGCGCACCTTCAAGCAGCTGTTGTCGAGTTTTCAGCGTAACCGCGATCTGGTTAGCGTCGGCGCGTATGCCAAAGGCAGCGATCCGATGCTCGATAAAGCCATCGCCCTGTGGCCg                                 >  1:809182/1‑131 (MQ=255)

                                                                                                                cgcgcgAGTGCGCACCTTCAAGCAGCTGTTGTCGAGTTTTCAGCGTAACCGCGATCTGGTTAGCGTCGGCGCGTATGCCAAAGGCAGCGATCCGATGCTCGATAAAGCCATCGCCCTGTGGCCGCAGCTGGAGGGCTAtt                 <  2:621824/140‑1 (MQ=255)

                                                                                                                cgcgcgAGTGCGCACCTTCAAGCAGCTGTTGTCGAGTTTTCAGCGTAACCGCGATCTGGTTAGCGTCGGCGCGTATGCCAAAGGCAGCGATCCGATGCTCGATAAAGCCATCGCCCTGTGGCCGCAGCTGGAGGGCTAtt                 <  2:929331/140‑1 (MQ=255)

                                                                                                                  cgcgAGTGCGCACCTTCAAGCAGCTGTTGTCGAGTTTTCAGCGTAACCGCGATCTGGTTAGCGTCGGCGCGTATGCCAAAGGCAGCGATCCGATGCTCGATAAAGCCATCGCCCTGTGGCCGCAGCTGGAGGGCTATTTg               >  1:534659/1‑140 (MQ=255)

                                                                                                                     gAGTGCGCACCTTCAAGCAGCTGTTGTCGAGTTTTCAGCGTAACCGCGATCTGGTTAGCGTCGGCGCGTATGCCAAAGGCAGCGATCCGATGCTCGATAAAGCCATCGCCCTGTGGCCGCAGCTGGAGGGCTATTTGcaa            >  1:1159223/1‑140 (MQ=255)

                                                                                                                        tGCGCACCTTCAAGCAGCTGTTGTCGAGTTTTCAGCGTAACCGCGATCTGGTTAGCGTCGGCGCGTATGCCAAAGGCAGCGATCCGATGCTCGATAAAGCCATCGCCCTGTGGCCGCAGCTGGa                         <  2:53276/124‑1 (MQ=255)

                                                                                                                        tGCGCACCTTCAAGCAGCTGTTGTCGAGTTTTCAGCGTAACCGCGATCTGGTTAGCGTCGGCGCGTATGCCAAAGGCAGCGATCCGATGCTCGATAAAGCCATCGCCCTGTGGCCGCAGCTGGa                         >  1:53276/1‑124 (MQ=255)

                                                                                                                          cgcACCTTCAAACAGCTGTTGTCGAGTTGTCAGCGGAACCGCGATCTGGTTAGCGTCGGCGCGTATGCCAAAGGCAGTGAGCCGATGCTCGATAAAGCCATCGCCCTGTGGCCGCAGCTGGAGGGCTATTTGCAACAAgg       <  2:846758/140‑1 (MQ=255)

                                                                                                                           gcACCTTCAAGCAGCTGTTGTCGAGTTTTCAGCGTAACCGCGATCTGGTTAGCGTCGGCGCGTATGCCAAAGGCAGCGATCCGATGCTCGATAAAGCCATCGCCCTGTGGCCGCAGCTGGAGGGCTATTTGCAACAAGGc      >  1:579213/1‑140 (MQ=255)

                                                                                                                               cTTCAAGCAGCTGTTGTCGAGTTTTCAGCGTAACCGCGATCTGGTTAGCGTCGGCGCGTATGCCAAAGGCAGCGATCCGATGCTCGATAAAGCCATCGCCCTGTGGCCGCAGCTGGAGGGCTATTTGCAACAAGGCAttt  >  1:1050787/1‑140 (MQ=255)

ACGGTCACATTGTGCTGTCTCGCCGACTGGCGGAAGCCGGGCACTATCCGGCTATCGATATTGAAGCGTCGATCAGCCGCGCAATGACGGCGTTGATCAGTGAGCAACATTACGCGCGAGTGCGCACCTTCAAACAGCTGTTGTCGAGTTTTCAGCGTAACCGCGATCTGGTTAGCGTCGGCGCGTATGCCAAAGGCAGCGATCCGATGCTCGATAAAGCCATCGCCCTGTGGCCGCAGCTGGAGGGCTATTTGCAACAAGGCATTT  >  NC_000913/2017596‑2017862

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