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 I181 R1	159	32.7	1279082	96.9%	1239430	121.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	609,496	A→C	L33F (TTA→TTC)	ybdZ →	enterobactin biosynthesis protein YbdZ

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	609,496	0	A	C	100.0%	123.3 / NA	34	L33F (TTA→TTC)	ybdZ	enterobactin biosynthesis protein YbdZ
Reads supporting (aligned to +/- strand): ref base A (0/0); new base C (19/15); total (19/15)

CCTCTGGCAACCACTTTTCCATGACAGGAGTTGAATATGGCATTCAGTAATCCCTTCGATGATCCGCAGGGAGCGTTTTACATATTGCGCAATGCGCAGGGGCAATTCAGTCTGTGGCCGCAACAATGCGTCTTACCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACAGGCGTCCTGCCAGCAGTGGCTGGAAGCCCACTGGCGTACTCTGACACCGACGAATTTTACCCAGTTGCAGGAGGCACAATGAGCCAGCATTTACCTT  >  NZ_CP009273/609362‑609631

ccTCTGGCAACCACTTTTCCATGACAGGAGTTGAATATGGCATTCAGTAATCCCTTCGATGATCCGCAGGGAGCGTTTTACATATTGCGCAATGCGCAGGGGCAATTCAGTCTGTGGCCGCAACAATGCGTCTTCCCgg                                                                                                                                     <  1:340227/139‑1 (MQ=255)

 ctctGGCAACCACTTTTCCATGACAGGAGTTGAATATGGCATTCAGTAATCCCTTCGATGATCCGCAGGGAGCGTTTTACATATTGCGCAATGCGCAGGGGCAATTCAGTCTGTGGCCGCAACAATGCGTCTTCCCgg                                                                                                                                     >  2:451202/1‑138 (MQ=255)

                          ggAGTTGAATATGGCATTCAGTAATCCCTTCGATGATCCGCAGGGAGCGTTTTACATATTGCGCAATGCGCAGGGGCAATTCAGTCTGTGGCCGCAACAATGCGTCTTCCCGGCAGGCTGGGACATTGTGTGTCAGCCg                                                                                                           <  1:345466/139‑1 (MQ=255)

                             gTTGAATATGGCATTCAGTAATCCCTTCGATGATCCGCAGGGAGCGTTTTACATATTGCGCAATGCGCAGGGGCAATTCAGTCTGTGGCCGCAACAATGCGTCTTCCCGGCAGGCTGGGACATTGTGTGTCAGCCGCAg                                                                                                        >  2:135715/1‑139 (MQ=255)

                                          ttCAGTAATCCCTTCGATGATCCGCAGGGAGCGTTTTACATATTGCGCAATGCGCAGGGGCAATTCAGTCTGTGGCCGCAACAATGCGTCTTCCCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACAGGCGTCCt                                                                                           <  1:112068/139‑1 (MQ=255)

                                               tAATCCCTTCGATGATCCGCAGGGAGCGTTTTACATATTGCGCAATGCGCAGGGGCAATTCAGTCTGTGGCCGCAACAATGCGTCTTCCCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACAGGCGTCCTGCcag                                                                                      >  2:231183/1‑139 (MQ=255)

                                                    ccTTCGATGATCCGCAGGGAGCGTTTTACATATTGCGCAATGCGCAGGGGCAATTCAGTCTGTGGCCGCAACAATGCGTCTTCCCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACAGGCGTCCTGCCAGCAGTg                                                                                 <  2:298197/139‑1 (MQ=255)

                                                    ccTTCGATGATCCGCAGGGAGCGTTTTACATATTGCGCAATGCGCAGGGGCAATTCAGTCTGTGGCCGCAACAATGCGTCTTCCCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACAGGCGTCCTGCCAGCAGTg                                                                                 >  1:587573/1‑139 (MQ=255)

                                                       tCGATGATCCGCAGGGAGCGTTTTACATATTGCGCAATGCGCAGGGGCAATTCAGTCTGTGGCCGCAACAATGCGTCTTCCCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACAGGCGTCCTGCCAGCAGTGGCt                                                                              >  1:154681/1‑139 (MQ=255)

                                                         gatgatCCGCAGGGAGCGTTTTACATATTGCGCAATGCGCAGGGGCAATTCAGTCTGTGGCCGCAACAATGCGTCTTCCCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACAGGCGTCCTGCCAGCAGTGGCTgg                                                                            <  2:352703/139‑1 (MQ=255)

                                                         gatgatCCGCAGGGAGCGTTTTACATATTGCGCAATGCGCAGGGGCAATTCAGTCTGTGGCCGCAACAATGCGTCTGCCCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACAGGCGTCCTGCCAGCAGTGGCTgg                                                                            <  1:617905/139‑1 (MQ=255)

                                                                cGCAGGGAGCGTTTTACATATTGCGCAATGCGCAGGGGCAATTCAGTCTGTGGCCGCAACAATGCGTCTTCCCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACAGGCGTCCTGCCAGCAGTGGCTGGAAGCCCa                                                                     <  2:154681/139‑1 (MQ=255)

                                                                      gAGCGTTTTACATATTGCGCAATGCGCAGGGGCAATTCAGTCTGTGGCCGCAACAATGCGTCTTCCCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACAGGCGTCCTGCCAGCAGTGGCTGGAAGCCCACTGGCg                                                               <  2:587573/139‑1 (MQ=255)

                                                                                     tGCGCAATGCGCAGGGGCAATTCAGTCTGTGGCCGCAACAATGCGTCTTCCCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACAGGCGTCCTGCCAGCAGTGGCTGGAAGCCCACTGGCGTACTCTGACACcgac                                                >  1:86835/1‑139 (MQ=255)

                                                                                       cgcAATGCGCAGGGGCAATTCAGTCTGTGGCCGCAACAATGCGTCTTCCCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACAGGCGTCCTGCCAGCAGTGGCTGGAAGCCCACTGGCGTACTCTGACACcgacg                                               >  1:505046/1‑138 (MQ=255)

                                                                                          aaTGCGCAGGGGCAATTCAGTCTGTGGCCGCAACAATGCGTCTTCCCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACAGGCGTCCTGCCAGCAGTGGCTGGAAGCCCACTGGCGTACTCTGACACCGACGAAtt                                           >  2:52282/1‑139 (MQ=255)

                                                                                               gcAGGGGCAATTCAGTCTGTGGCCGCAACAATGCGTCTTCCCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACAGGCGTCCTGCCAGCAGTGGCTGGAAGCCCACTGGCGTACTCTGACACCGACGAATTTTAcc                                      <  1:231183/139‑1 (MQ=255)

                                                                                                 aGGGGCAATTCAGTCTGTGGCCGCAACAATGCGTCTTCCCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACAGGCGTCCTGCCAGCAGTGGCTGGAAGCCCACTGGCGTACTCTGACACCGACGAATTTTAcc                                      >  1:453423/1‑137 (MQ=255)

                                                                                                 aGGGGCAATTCAGTCTGTGGCCGCAACAATGCGTCTTCCCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACAGGCGTCCTGCCAGCAGTGGCTGGAAGCCCACTGGCGTACTCTGACACCGACGAATTTTAcc                                      >  2:360366/1‑137 (MQ=255)

                                                                                                      cAATTCAGTCTGTGGCCGCAACAATGCGTCTTCCCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACAGGCGTCCTGCCAGCAGTGGCTGGAAGCCCACTGGCGTACTCTGACACCGACGAATTTTACCCAGTTg                                >  1:372772/1‑138 (MQ=255)

                                                                                                        aTTCAGTCTGTGGCCGCAACAATGCGTCTTCCCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACAGGCGTCCTGCCAGCAGTGGCTGGAAGCCCACTGGCGTACTCTGACACCGACGAATTTTACCCAGTTGCag                             >  1:553703/1‑139 (MQ=255)

                                                                                                        aTTCAGTCTGTGGCCGCAACAATGCGTCTTCCCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACAGGCGTCCTGCCAGCAGTGGCTGGAAGCCCACTGGCGTACTCTGACACCGACGAATTTTACCCAGTTGCag                             >  1:620482/1‑139 (MQ=255)

                                                                                                         ttCAGTCTGTGGCCGCAACAATGCGTCTTCCCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACAGGCGTCCTGCCAGCAGTGGCTGGAAGCCCACTGGCGTACTCTGACACCGACGAATTTTACCCAGTTGCagg                            <  2:553703/139‑1 (MQ=255)

                                                                                                             gTCTGTGGCCGCAACAATGCGTCTTCCCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACAGGCGTCCTGCCAGCAGTGGCTGGAAGCCCACTGGCGTACTCTGACACCGACGAATTTTACCCAGTTGCaggagg                         >  1:119616/1‑138 (MQ=255)

                                                                                                                  tgGCCGCAACAATGCGTCTTCCCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACAGGCGTCCTGCCAGCAGTGGCTGGAAGCCCACTGGCGTACTCTGACACCGACGAATTTTACCCAGTTGCAGGAGGcaca                     <  2:505046/137‑1 (MQ=255)

                                                                                                                              tGCGTCTTCCCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACAGGCGTCCTGCCAGCAGTGGCTGGAAGCCCACTGGCGTACTCTGACACCGACGAATTTTACCCAGTTGCaggagg                         <  2:449680/121‑1 (MQ=255)

                                                                                                                              tGCGTCTTCCCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACAGGCGTCCTGCCAGCAGTGGCTGGAAGCCCACTGGCGTACTCTGACACCGACGAATTTTACCCAGTTGCaggagg                         >  1:449680/1‑121 (MQ=255)

                                                                                                                                   cTTCCCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACAGGCGTCCTg                                                                                          <  2:175640/51‑1 (MQ=255)

                                                                                                                                   cTTCCCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACAGGCGTCCTg                                                                                          >  1:175640/1‑51 (MQ=255)

                                                                                                                                   cTTCCCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACAGGCGTCCTGCCAGCAGTGGCTGGAAGCCCACTGGCg                                                               >  1:25283/1‑78 (MQ=255)

                                                                                                                                   cTTCCCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACAGGCGTCCTGCCAGCAGTGGCTGGAAGCCCACTGGCg                                                               <  2:25283/78‑1 (MQ=255)

                                                                                                                                   cTTCCCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACAGGCGTCCTGCCAGCAGTGGCTGGAAGCCCACTGGCGTACTCTGACACCGACGAATTTTACCCAGTTGCAGGAGGCACAATGAGc               >  2:569700/1‑126 (MQ=255)

                                                                                                                                   cTTCCCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACAGGCGTCCTGCCAGCAGTGGCTGGAAGCCCACTGGCGTACTCTGACACCGACGAATTTTACCCAGTTGCAGGAGGCACAATGAGc               <  1:569700/126‑1 (MQ=255)

                                                                                                                                   cTTCCCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACAGGCGTCCTGCCAGCAGTGGCTGGAAGCCCACTGGCGTACTCTGACACCGACGAATTTTACCCAGTTGCAGGAGGCACAATGAGCCAGCATTTAACtt  >  2:137525/1‑139 (MQ=255)

CCTCTGGCAACCACTTTTCCATGACAGGAGTTGAATATGGCATTCAGTAATCCCTTCGATGATCCGCAGGGAGCGTTTTACATATTGCGCAATGCGCAGGGGCAATTCAGTCTGTGGCCGCAACAATGCGTCTTACCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACAGGCGTCCTGCCAGCAGTGGCTGGAAGCCCACTGGCGTACTCTGACACCGACGAATTTTACCCAGTTGCAGGAGGCACAATGAGCCAGCATTTACCTT  >  NZ_CP009273/609362‑609631

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

BRESEQ :: bam2aln output

ACCTCTGGCAACCACTTTTCCATGACAGGAGTTGAATATGGCATTCAGTAATCCCTTCGATGATCCGCAGGGAGCGTTTTACATATTGCGCAATGCGCAGGGGCAATTCAGTCTGTGGCCGCAACAATGCGTCTTACCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACAGGCGTCCTGCCAGCAGTGGCTGGAAGCCCACTGGCGTACTCTGACACCGACGAATTTTACCCAGTTGCAGGAGGCACAATGAGCCAGCATTTACCTTT  >  NZ_CP009273/609361‑609632

ACCTCTGGCAACCACTTTTCCATGACAGGAGTTGAATATGGCATTCAGTAATCCCTTCGATGATCCGCAGGGAGCGTTTTACATATTGCGCAATGCGCAGGGGCAATTCAGTCTGTGGCCGCAACAATGCGTCTTCCCGGCAGGCTGGGAC                                                                                                                           <  SRR3722135.345063/151‑1 (MQ=60)

                          AGGAGTTGAATATGGCATTCAGTAATCCCTTCGATGATCCGCAGGGAGCGTTTTACATATTGCGCAATGCGCAGGGGCAATTCAGTCTGTGGCCGCAACAATGCGTCTTCCCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACAGGC                                                                                                 <  SRR3722135.350363/151‑1 (MQ=60)

                                          ATTCAGTAATCCCTTCGATGATCCGCAGGGAGCGTTTTACATATTGCGCAATGCGCAGGGGCAATTCAGTCTGTGGCCGCAACAATGCGTCTTCCCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACAGGCGTCCTGCCAGCAGTGG                                                                                 <  SRR3722135.113589/151‑1 (MQ=60)

                                          ATTCAGTAATCCCTTCGATGATCCGCAGGGAGCGTTTTACATATTGCGCAATGCGCAGGGGCAATTCAGTCTGTGGCCGCAACAATGCGTCTTCCCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACAGGCGTCCTGCCAGCAGTGG                                                                                 >  SRR3722135.595273/1‑151 (MQ=60)

                                             CAGTAATCCCTTCGATGATCCGCAGGGAGCGTTTTACATATTGCGCAATGCGCAGGGGCAATTCAGTCTGTGGCCGCAACAATGCGTCTTCCCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACAGGCGTCCTGCCAGCAGTGGCTG                                                                              >  SRR3722135.156821/1‑151 (MQ=60)

                                                         CGATGATCCGCAGGGAGCGTTTTACATATTGCGCAATGCGCAGGGGCAATTCAGTCTGTGGCCGCAACAATGCGTCTGCCCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACAGGCGTCCTGCCAGCAGTGGCTGGAAGCCCACTGG                                                                  <  SRR3722135.626005/151‑1 (MQ=60)

                                                                           GTTTTACATATTGCGCAATGCGCAGGGGCAATTCAGTCTGTGGCCGCAACAATGCGTCTTCCCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACAGGCGTCCTGCCAGCAGTGGCTGGAAGCCCACTGGCGTACTCTGACACCGACG                                                >  SRR3722135.87997/1‑151 (MQ=60)

                                                                             TTTACATATTGCGCAATGCGCAGGGGCAATTCAGTCTGTGGCCGCAACAATGCGTCTTCCCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACAGGCGTCCTGCCAGCAGTGGCTGGAAGCCCACTGGCGTACTCTGACACCGACGA                                               >  SRR3722135.511814/1‑150 (MQ=60)

                                                                                       GCGCAATGCGCAGGGGCAATTCAGTCTGTGGCCGCAACAATGCGTCTTCCCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACAGGCGTCCTGCCAGCAGTGGCTGGAAGCCCACTGGCGTACTCTGACACCGACGAATTTTACCC                                      >  SRR3722135.459557/1‑149 (MQ=60)

                                                                                            ATGCGCAGGGGCAATTCAGTCTGTGGCCGCAACAATGCGTCTTCCCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACAGGCGTCCTGCCAGCAGTGGCTGGAAGCCCACTGGCGTACTCTGACACCGACGAATTTTACCCAGTTGC                                >  SRR3722135.377990/1‑150 (MQ=60)

                                                                                              GCGCAGGGGCAATTCAGTCTGTGGCCGCAACAATGCGTCTTCCCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACAGGCGTCCTGCCAGCAGTGGCTGGAAGCCCACTGGCGTACTCTGACACCGACGAATTTTACCCAGTTGCAGG                             >  SRR3722135.628608/1‑151 (MQ=60)

                                                                                              GCGCAGGGGCAATTCAGTCTGTGGCCGCAACAATGCGTCTTCCCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACAGGCGTCCTGCCAGCAGTGGCTGGAAGCCCACTGGCGTACTCTGACACCGACGAATTTTACCCAGTTGCAGG                             >  SRR3722135.561036/1‑151 (MQ=60)

                                                                                               CGCAGGGGCAATTCAGTCTGTGGCCGCAACAATGCGTCTTCCCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACAGGCGTCCTGCCAGCAGTGGCTGGAAGCCCACTGGCGTACTCTGACACCGACGAATTTTACCCAGTTGCAGGA                            <  SRR3722135.234433/151‑1 (MQ=60)

                                                                                                   GGGGCAATTCAGTCTGTGGCCGCAACAATGCGTCTTCCCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACAGGCGTCCTGCCAGCAGTGGCTGGAAGCCCACTGGCGTACTCTGACACCGACGAATTTTACCCAGTTGCAGGAGGC                         >  SRR3722135.121285/1‑150 (MQ=60)

                                                                                                                    GGCCGCAACAATGCGTCTTCCCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACAGGCGTCCTGCCAGCAGTGGCTGGAAGCCCACTGGCGTACTCTGACACCGACGAATTTTACCCAGTTGCAGGAGGCACAATGAGCCctgtctct       >  SRR3722135.455767/1‑143 (MQ=60)

                                                                                                                      CAGCAACAATGCGTCTTCCCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACAGGCGTCCTGCCAGCAGTGGCTGGAAGCCCACTGGCGTACTCTGACACCGACGAATTTTACCCAGTTGCAGGAGGCACAATGAGCCAGCATTTACC     <  SRR3722135.577199/151‑1 (MQ=60)

                                                                                                                         CAACAATGCGTCTTCCCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACAGGCGTCCTGCCAGCAGTGGCctgtctcttatacacatctccgagcccacgagaccgtactagatctcgtatgccgtcttctgcttgaaaaaaaaaaa   >  SRR3722135.178076/1‑73 (MQ=60)

                                                                                                                         CAACAATGCGTCTTCCCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACAGGCGTCCTGCCAGCAGTGGCTGGAAGCCCACTGGCGTACTCTGACACCtgtctcttatacacatctccgagcccacgagaccgtactagatctcgtat  >  SRR3722135.25616/1‑101 (MQ=60)

ACCTCTGGCAACCACTTTTCCATGACAGGAGTTGAATATGGCATTCAGTAATCCCTTCGATGATCCGCAGGGAGCGTTTTACATATTGCGCAATGCGCAGGGGCAATTCAGTCTGTGGCCGCAACAATGCGTCTTACCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACAGGCGTCCTGCCAGCAGTGGCTGGAAGCCCACTGGCGTACTCTGACACCGACGAATTTTACCCAGTTGCAGGAGGCACAATGAGCCAGCATTTACCTTT  >  NZ_CP009273/609361‑609632

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`