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 F5 I184 R1	278	29.6	1166432	97.3%	1134938	124.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	885,786	T→G	L81R (CTG→CGG)	ybjM →	inner membrane protein YbjM

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	885,786	0	T	G	100.0%	118.8 / NA	34	L81R (CTG→CGG)	ybjM	inner membrane protein YbjM
Reads supporting (aligned to +/- strand): ref base T (0/0); new base G (15/19); total (15/19)

TCATTCTTCCTGGAGCAGTCGCCAGCTTCTTTTCACAGCGTAGAGAAGTCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCTGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTACTAAGCGCGGTGTTCTGGTGTGCGCTGGGGGCACTGTGTTTCTTATTTATCAGTAGTTTGTTTAAACCACAGCACAGAAAAA  >  NZ_CP009273/885678‑885914

tCATTCTTCCTGGAGCAGTCGCCAGCTTCTTTTCACAGCGTAGAGAAGTCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGc                                                                                                     <  1:114284/138‑1 (MQ=255)

     cttcCTGGAGCAGTCGCCAGCTTCTTTTCACAGCGTAGAGAAGTCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAagag                                                                                                <  1:353732/138‑1 (MQ=255)

            gAGCAGTCGCCAGCTTCTTTTCACAGCGTAGAGAAGTCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCa                                                                                          <  2:370749/137‑1 (MQ=255)

            gAGCAGTCGCCAGCTTCTTTTCACAGCGTAGAGAAGTCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCa                                                                                          <  1:181973/137‑1 (MQ=255)

                  tCGCCAGCTTCTTTTCACAGCGTAGAGAAGTCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCa                                                                                          <  2:165532/131‑1 (MQ=255)

                  tCGCCAGCTTCTTTTCACAGCGTAGAGAAGTCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCa                                                                                          >  1:165532/1‑131 (MQ=255)

                       aGCTTCTTTTCACAGCGTAGAGAAGTCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTACTAAgcg                                                                             <  2:123963/139‑1 (MQ=255)

                         cttcttTTCACAGCGTAGAGAAGTCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTACTAAGcgcg                                                                           <  1:536106/139‑1 (MQ=255)

                                   caGCGTAGAGAAGTCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTACTAAGCGCGGTGTTCTGgt                                                                 <  2:97174/139‑1 (MQ=255)

                                      cGTAGAGAAGTCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTACTAAGCGCGGTGTTCTGGtgtg                                                              >  2:415115/1‑139 (MQ=255)

                                                tCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGc                                                                                                     <  1:1159/90‑1 (MQ=255)

                                                tCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGc                                                                                                     >  2:1159/1‑90 (MQ=255)

                                                tCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCa                                                                                          >  2:76359/1‑101 (MQ=255)

                                                tCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCa                                                                                          <  1:76359/101‑1 (MQ=255)

                                                tCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTACTAAGCGCGGTGTTCTGGTGTGCGCTggggg                                                     >  1:124871/1‑138 (MQ=255)

                                                tCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTACTAAGCGCGGTGTTCTGGTGTGCGCTggggg                                                     >  1:496846/1‑138 (MQ=255)

                                                tCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTACTAAGCGCGGTGTTCTGGTGTGCGCTggggg                                                     >  2:242011/1‑138 (MQ=255)

                                                  cTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGc                                                                                                     <  1:147267/88‑1 (MQ=255)

                                                  cTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGc                                                                                                     >  2:147267/1‑88 (MQ=255)

                                                  cTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCCTGGTTACTAAGcgcg                                                                           >  1:174523/1‑114 (MQ=255)

                                                  cTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTACTAAGcgcg                                                                           <  2:174523/114‑1 (MQ=255)

                                                  cTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTACTAAGCGCGGTGTTCTGgt                                                                 >  1:232531/1‑124 (MQ=255)

                                                  cTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTACTAAGCGCGGTGTTCTGgt                                                                 <  2:232531/124‑1 (MQ=255)

                                                  cTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGGTACTAAGCGCGGTGTTCTGGTGGGCGCTGGGGGCAc                                                  >  1:163391/1‑139 (MQ=255)

                                                     aaaCCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTACTAAGCGCGGTGTTCTGGTGTGCGCTGGGGGCACt                                                 <  2:124871/137‑1 (MQ=255)

                                                        ccTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTACTAAGCGCGGTGTTCTGGTGTGCGCTGGGGGCACTGTGtt                                            <  2:528249/139‑1 (MQ=255)

                                                                        tGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGc                                                                                                     >  2:133782/1‑66 (MQ=255)

                                                                        tGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGc                                                                                                     <  1:133782/66‑1 (MQ=255)

                                                                        tGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTACTAAGCGCGGTGTTCTGGTGTGCGCTGGGGGCACTGTGTTTCTTATTTATCagtag                            <  1:415115/139‑1 (MQ=255)

                                                                                                  aTTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGGATGGTTACTAAGCGCGGTGTTCTGGTGTGCGCTGGGGGCACTGTGTTTCTTATTTATCAGTAGTTTGTTTAAACCACAGCACAGaaaa   >  1:14383/1‑138 (MQ=255)

                                                                                                  aTTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTACTAAGCGCGGTGTTCTGGTGTGCGCTGGGGGCACTGTGTTTCTTATTTATCAGTAGTTTGTTTAAACCACAGCACAGaaaaa  <  2:433155/139‑1 (MQ=255)

                                                                                                  aTTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTACTAAGCGCGGTGTTCTGGTGTGCGCTGGGGGCACTGTGTTTCTTATTTATCAGTAGTTTGTTTAAACCACAGCACAGaaaa   >  1:182881/1‑138 (MQ=255)

                                                                                                    tATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTACTAAGCGCGGTGTTCTGGTGTGCGCTGGGGGCACTGTGTTTCt                                         <  1:537601/98‑1 (MQ=255)

                                                                                                    tATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTACTAAGCGCGGTGTTCTGGTGTGCGCTGGGGGCACTGTGTTTCt                                         >  2:537601/1‑98 (MQ=255)

TCATTCTTCCTGGAGCAGTCGCCAGCTTCTTTTCACAGCGTAGAGAAGTCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCTGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTACTAAGCGCGGTGTTCTGGTGTGCGCTGGGGGCACTGTGTTTCTTATTTATCAGTAGTTTGTTTAAACCACAGCACAGAAAAA  >  NZ_CP009273/885678‑885914

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 29 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

BRESEQ :: bam2aln output

TTTCATTCTTCCTGGAGCAGTCGCCAGCTTCTTTTCACAGCGTAGAGAAGTCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCTGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTACTAAGCGCGGTGTTCTGGTGTGCGCTGGGGGCACTGTGTTTCTTATTTATCAGTAGTTTGTTTAAACCACAGCACAGAAAAAATCAGTAA  >  NZ_CP009273/885676‑885922

gtacggtctcgtgggctcggagatgtgtataagagacagGCGTAGAGAAGTCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCA                                                                                                  <  SRR3722139.1170/112‑1 (MQ=60)

gcagaagacggcatacgagatctagtacggtctcgtgggctcggagatgtgtataagagacagGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCA                                                                                                  <  SRR3722139.135411/88‑1 (MQ=60)

 agtacggtctcgtgggctcggagatgtgtataagagacagGTAGAGAAGTCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCA                                                                                                  <  SRR3722139.149059/110‑1 (MQ=60)

 TTCATTCTTCCTGGAGCAGTCGCCAGCTTCTTTTCACAGCGTAGAGAAGTCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCA                                                                                                  <  SRR3722139.115661/150‑1 (MQ=60)

      TCTTCCTGGAGCAGTCGCCAGCTTCTTTTCACAGCGTAGAGAAGTCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTT                                                                                             <  SRR3722139.358007/150‑1 (MQ=60)

         TCCTGGAGCAGTCGCCAGCTTCTTTTCACAGCGTAGAGAAGTCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGGTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTACT                                                                                          >  SRR3722139.167594/1‑150 (MQ=60)

            gggctcggagatgtgtataagagacagGCGTAGAGAAGTCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTACTAAG                                                                                       <  SRR3722139.77242/123‑1 (MQ=60)

             GGAGCAGTCGCCAGCTTCTTTTCACAGCGTAGAGAAGTCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTACTAAG                                                                                       <  SRR3722139.184224/149‑1 (MQ=60)

                          GCTTCTTTTCACAGCGTAGAGAAGTCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTACTAAGCGCGGTGTTCTGGTG                                                                        <  SRR3722139.542262/151‑1 (MQ=60)

                                       GCGTAGAGAAGTCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTACTAAGCGCGGTGTTCTGGTGTGCGCTGGGGGC                                                            >  SRR3722139.502593/1‑150 (MQ=60)

                                       GCGTAGAGAAGTCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTACTAAGCGCGGTGTTCTGGTGTGCGCTGGGGGC                                                            >  SRR3722139.126385/1‑150 (MQ=60)

                                         GTAGAGAAGTCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCCTGGTTACTAAGCGCGGTGTTCTGGTGctgtctcttatacac                                                         >  SRR3722139.176703/1‑136 (MQ=60)

                                         GTAGAGAAGTCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTACTAAGCGCGGTGTTCTGGTGTGCGCTGGGGctgtc                                                         >  SRR3722139.235400/1‑146 (MQ=60)

                                         GTAGAGAAGTCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGGTACTAAGCGCGGTGTTCTGGTGGGCGCTGGGGGCACT                                                         >  SRR3722139.165404/1‑151 (MQ=60)

                                          ggctcggagatgtgtataagagacaGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTACTAAGCGCGGTGTTCTGGTGTGCGCTGGGGGCACTG                                                        <  SRR3722139.17565/126‑1 (MQ=60)

                                                             cgtgggctcggagatgtgtataagagacagTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTACTAAGCGCGGTGTTCTGGTGTGCGCTGGGGGCACTGTGTTTCTTATTTATCAGT                                      <  SRR3722139.543772/120‑1 (MQ=60)

                                                                         ATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTACTAAGCGCGGTGTTCTGGTGTGCGCTGGGGGCACTGTGTTTCTTATTTATCAGTAGTTTGTTTAAAC                         <  SRR3722139.420042/151‑1 (MQ=60)

                                                                                         GTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGGATGGTTACTAAGCGCGGTGTTCTGGTGTGCGCTGGGGGCACTGTGTTTCTTATTTATCAGTAGTTTGTTTAAACCACAGCACAGAAAAA          >  SRR3722139.14529/1‑150 (MQ=60)

                                                                                         GTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTACTAAGCGCGGTGTTCTGGTGTGCGCTGGGGGCACTGTGTTTCTTATTTATCAGTAGTTTGTTTAAACCACAGCACAGAAAAA          >  SRR3722139.185142/1‑150 (MQ=60)

                                                                                                GCTCATTATGCGGCGGTTTTTTTCAGCGACGCCCTCATTCTGGCAAGAGCTGGCCTGGTTACTAAACGCGGTGTTCTGGTGTGCGCCGGGGGCACTGTGTTTCTTATTTATCcagagtttggttaaaccctgtctcttatacccatctccg  >  SRR3722139.447121/1‑112 (MQ=60)

TTTCATTCTTCCTGGAGCAGTCGCCAGCTTCTTTTCACAGCGTAGAGAAGTCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCTGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTACTAAGCGCGGTGTTCTGGTGTGCGCTGGGGGCACTGTGTTTCTTATTTATCAGTAGTTTGTTTAAACCACAGCACAGAAAAAATCAGTAA  >  NZ_CP009273/885676‑885922

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`