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	626,664	T→C	S439P (TCG→CCG)	cstA →	pyruvate/proton symporter CstA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	626,664	0	T	C	100.0%	82.7 / NA	23	S439P (TCG→CCG)	cstA	pyruvate/proton symporter CstA
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (10/13); total (10/13)

AACAGCCCGATGGCGGTGCTGGCTCCGGCAGGGACGGCGGATGTGGTCGCTTCTGCCGCGCAGGTGGTGAGTAGCTGGGGCTTTAGCATTACACCAGATACGCTAAACCAGATTGCCAGCGAAGTGGGTGAACAGTCGATCATTTCCCGTGCGGGCGGTGCGCCGACGCTGGCGGTGGGGATGGCCTACATTCTGCACGGCGCGCTGGGCGGCATGATGGATGTGGCGTTCTGGTATCACTTCGCCATTTTGTTTGAAGCACTG  >  NZ_CP009273/626529‑626792

aaCAGCCCGATGGCGGTGCTGGCTCCGGCAGGGACGGCGGATGTGGTCGCTTCTGCCGCGCAGGTGGTGAGTAGCTGGGGCTTTAGCATTACACCAGATACGCTAAACCAGATTGCCAGCGAAGTGGGTGAACAGCCGa                                                                                                                               >  1:615773/1‑139 (MQ=255)

     cccGATGGCGGTGCTGGCTCCGGCAGGGACGGCGGATGTGGTCGCTTCTGCCGCGCAGGTGGTGAGTAGCTGGGGCTTTAGCATTACACCAGATACGCTAAACCAGATTGCCAGCGAAGTGGGGGAACAGCCGATCAtt                                                                                                                          >  2:316478/1‑139 (MQ=255)

                                         tgtgGTCGCTTCTGCCGCGCAGGTGGTGAGTAGCTGGGGCTTTAGCATTACACCAGATACGCTAAACCAGATTGCCAGCGAAGTGGGTGAACAGCCGATCATTTCCCGTGCGGGCGGTGCGCCGACGCTGGCGGTgggg                                                                                      <  2:559150/139‑1 (MQ=255)

                                         tgtgGTCGCTTCTGCCGCGCAGGTGGTGAGTAGCTGGGGCTTTAGCATTACACCAGATACGCTAAACCAGATTGCCAGCGAAGTGGGTGAACAGCCGATCATTTCCCGTGCGGGCGGTGCGCCGACGCTGGCGGTgggg                                                                                      <  2:206639/139‑1 (MQ=255)

                                         tgtgGTCGCTTCTGCCGCGCAGGTGGTGAGTAGCTGGGGCTTTAGCATTACACCAGATACGCTAAACCAGATTGCCAGCGAAGTGGGTGAACAGCCGATCATTTCCCGTGCGGGCGGTGCGCCGACGCTGGCGGTgggg                                                                                      <  2:111489/139‑1 (MQ=255)

                                                gCTTCTGCCGCGCAGGTGGTGAGTAGCTGGGGCTTTAGCATTACACCAGATACGCTAAACCAGATTGCCAGCGAAGTGGGTGAACAGCCGATCATTTCCCGTGCGGGCGGTGCGCCGACGCTGGCGGTGGGGATGGCCt                                                                               <  1:22946/139‑1 (MQ=255)

                                                 cTTCTGCCGCGCAGGTGGTGAGTAGCTGGGGCTTTAGCATTACACCAGATACGCTAAACCAGATTGCCAGCGAAGTGGGTGAACAGCCGATCATTTCCCGTGCGGGCGGTGCGCCGACGCTGGCGGTGGGGATGGCCTa                                                                              >  2:197315/1‑139 (MQ=255)

                                                                      gTAGCTGGGGCTTTAGCATTACACCAGATACGCTAAACCAGATTGCCAGCGAAGTGGGTGAACAGCCGATCATTTCCCGTGCGGGCGGTGCGCCGACGCTGGCGGTGGGGATGGCCTACATTCTGCACGGCGCGCTggg                                                         <  1:519185/139‑1 (MQ=255)

                                                                               gCTTTAGCATTACACCAGATACGCTAAACCAGATTGCCAGCGAAGTGGGTGAACAGCCGATCATTTCCCGTGCGGGCGGTGCGCCGACGCTGGCGGTGGGGATGGCCTACATTCTGCACGGCGCGCTGGGCGGCatgat                                                >  2:347884/1‑139 (MQ=255)

                                                                                   tAGCATTACACCAGATACGCTAAACCAGATTGCCAGCGAAGTGGGTGAACAGCCGATCATTTCCCGTGCGGGCGGTGCGCCGACGCTGGCGGTGGGGATGGCCTACATTCTGCACGGCGCGCTGGGCGGCATgatggat                                            >  1:434693/1‑139 (MQ=255)

                                                                                      cATTACACCAGATACGCTAAACCAGATTGCCAGCGAAGTGGGTGAACAGCCGATCATTTCCCGTGCGGGCGGTGCGCCGACGCTGGCGGTGGGGATGGCCTACATTCTGCACGGCGCGCTGGGCGGCATGATGGAtgtg                                         <  1:193619/139‑1 (MQ=255)

                                                                                          acacCAGATACGCTAAACCAGATTGCCAGCGAAGTGGGTGAACAGCCGATCATTTCCCGTGCGGGCGGTGCGCCGACGCTGGCGGTGGGGATGGCCTACATTCTGCACGGCGCGCTGGGCGGCATGATGGATGTGGCg                                      <  2:616805/138‑1 (MQ=255)

                                                                                                gATACGCTAAACCAGATTGCCAGCGAAGTGGGTGAACAGCCGATCATTTCCCGTGCGGGCGGTGCGCCGACGCTGGCGGTGGGGAt                                                                                    <  1:365511/86‑1 (MQ=255)

                                                                                                gATACGCTAAACCAGATTGCCAGCGAAGTGGGTGAACAGCCGATCATTTCCCGTGCGGGCGGTGCGCCGACGCTGGCGGTGGGGAt                                                                                    >  2:365511/1‑86 (MQ=255)

                                                                                                gATACGCTAAACCAGATTGCCAGCGAAGTGGGTGAACAGCCGATCATTTCCCGTGCGGGCGGTGCGCCGACGCTGGCGGTGGGGATGGCCt                                                                               <  2:174103/91‑1 (MQ=255)

                                                                                                gATACGCTAAACCAGATTGCCAGCGAAGTGGGTGAACAGCCGATCATTTCCCGTGCGGGCGGTGCGCCGACGCTGGCGGTGGGGATGGCCt                                                                               >  1:174103/1‑91 (MQ=255)

                                                                                                gATACGCTAAACCAGATTGCCAGCGAAGTGGGTGAACAGCCGATCATTTCCCGTGCGGGCGGTGCGCCGACGCTGGCGGTGGGGATGGCCTACATTCTGCACGGCGCGCTGGGCGGCATGATGGAtgtg                                         >  2:229100/1‑129 (MQ=255)

                                                                                                gATACGCTAAACCAGATTGCCAGCGAAGTGGGTGAACAGCCGATCATTTCCCGTGCGGGCGGTGCGCCGACGCTGGCGGTGGGGATGGCCTACATTCTGCACGGCGCGCTGGGCGGCATGATGGAtgtg                                         <  1:229100/129‑1 (MQ=255)

                                                                                                     gCTAAACCAGATTGCCAGCGAAGTGGGTGAACAGCCGATCATTTCCCGTGCGGGCGGTGCGCCGACGCTGGCGGTGGGGATGGCCTACATTCTGCACGGCGCGCTGGGCGGCATGATGGATGTGGCGTTCTGGTATCAc                          >  1:452305/1‑139 (MQ=255)

                                                                                                              gATTGCCAGCGAAGTGGGTGAACAGCCGATCATTTCCCGTGCGGGCGGTGCGCCGACGCTGGCGGTGGGGATGGCCTACATTCTGCACGGCGCGCTGGGCGGCATGATGGATGTGGCGTTCTGGTATCACTTCGCCAtt                 <  1:253675/139‑1 (MQ=255)

                                                                                                                         aaGTGGGTGAACAGCCGATCATTTCCCGTGCGGGCGGTGCGCCGACGCTGGCGGTGGGGATGGCCTACATTCTGCACGGCGCGCTGGGCGGCATGATGGATGTGGCGTTCTGGTATCACTTCGCCATTTTGTTTGAAGc      <  2:434693/139‑1 (MQ=255)

                                                                                                                         aaGTGGGTGAACAGCCGATCATTTCCCGTGCGGGCGGTGCGCCGACGCTGGCGGTGGGGATGGCCTACATTCTGCACGGCGCGCTGGGCGGCATGATGGATGTGGCGTTCTGGTATCACTTCGCCATTTTGTTTGAAGc      <  2:452305/139‑1 (MQ=255)

                                                                                                                             gggTGAACAGCCGATCATTTCCCGTGCGGGCGGTGCGCCGACGCTGGCGGTGGGGATGGCCTACATTCTGCACGGCGCGCTGGGCGGCATGATGGATGTGGCGTTCTGGGATCACTTCGCCATTTTGTTTGAAGCACTg  >  2:28133/1‑139 (MQ=255)

AACAGCCCGATGGCGGTGCTGGCTCCGGCAGGGACGGCGGATGTGGTCGCTTCTGCCGCGCAGGTGGTGAGTAGCTGGGGCTTTAGCATTACACCAGATACGCTAAACCAGATTGCCAGCGAAGTGGGTGAACAGTCGATCATTTCCCGTGCGGGCGGTGCGCCGACGCTGGCGGTGGGGATGGCCTACATTCTGCACGGCGCGCTGGGCGGCATGATGGATGTGGCGTTCTGGTATCACTTCGCCATTTTGTTTGAAGCACTG  >  NZ_CP009273/626529‑626792

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 17 ≤` `ATCG/ATCG` `< 33 ≤` `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

ATTTTGCCATGAACAGCCCGATGGCGGTGCTGGCTCCGGCAGGGACGGCGGATGTGGTCGCTTCTGCCGCGCAGGTGGTGAGTAGCTGGGGCTTTAGCATTACACCAGATACGCTAAACCAGATTGCCAGCGAAGTGGGTGAACAGTCGATCATTTCCCGTGCGGGCGGTGCGCCGACGCTGGCGGTGGGGATGGCCTACATTCTGCACGGCGCGCTGGGCGGCATGATGGATGTGGCGTTCTGGTATCACTTCGCCATTTTGTTTGAAGCACTGTTTATTCTG  >  NZ_CP009273/626518‑626801

ATTTTGCCATGAACAGCCCGATGGCGGTGCTGGCTCCGGCAGGGACGGCGGATGTGGTCGCTTCTGCCGCGCAGGTGGTGAGTAGCTGGGGCTTTAGCATTACACCAGATACGCTAAACCAGATTGCCAGCGAAGTGGGTGAACAGCCGAT                                                                                                                                       >  SRR3722135.623806/1‑151 (MQ=60)

                                                        agtacggtctcgtgggctcggagatgtgtataagagacagGCATTACACCAGATACGCTAAACCAGATTGCCAGCGAAGTGGGTGAACAGCCGATCATTTCCCGTGCGGGCGGTGCGCCGACGCTGGCGGTGGGGATGGCCTACATTC                                                                                  <  SRR3722135.370660/108‑1 (MQ=60)

                                                          CGCTTCTGCCGCGCAGGTGGTGAGTAGCTGGGGCTTTAGCATTACACCAGATACGCTAAACCAGATTGCCAGCGAAGTGGGTGAACAGCCGATCATTTCCCGTGCGGGCGGTGCGCCGACGCTGGCGGTGGGGATGGCCTACATTCTGCAC                                                                             <  SRR3722135.23242/151‑1 (MQ=60)

                                                            CTTCTGCCGCGCAGGTGGTGAGTAGCTGGGGCTTTAGCATTACACCAGATACGCTAAACCAGATTGCCAGCGAAGTGGGTGAACAGCCGATCATTTCCCtgtctcttatacacatctccgagcccacgagaccgtactagatctcgtatgc                                                                           >  SRR3722135.61647/1‑99 (MQ=60)

                                                                                AGTAGCTGGGGCTTTAGCATTACACCAGATACGCTAAACCAGATTGCCAGCGAAGTGGGTGAACAGCCGATCATTTCCCGTGCGGGCGGTGCGCCGACGCTGGCGGTGGGGATGGCCTACATTCTGCACGGCGCGCTGGGCGGCATGATGG                                                       <  SRR3722135.526073/151‑1 (MQ=60)

                                                                                   AGCTGGGGCTTTAGCATTACACCAGATACGCTAAACCAGATTGCCAGCGAAGTGGGTGAACAGCCGATCATTTCCCGTGCGGGCGGTGCGCCGACGCTGGCGGTGGGGATGGCCTACATTCTGCACGGCGCGCTGGGCGGCATGATGGATG                                                    >  SRR3722135.440619/1‑151 (MQ=60)

                                                                                                GCATTACACCAGATACGCTAAACCAGATTGCCAGCGAAGTGGGTGAACAGCCGATCATTTCCCGTGCGGGCGGTGCGCCGACGCTGGCGGTGGGGATGGCCTACATTCTGCACctgtctcttatacacatctccgagcccacgagaccgt                                        >  SRR3722135.176517/1‑113 (MQ=60)

                                                                                                GCATTACACCAGATACGCTAAACCAGATTGCCAGCGAAGTGGGTGAACAGCCGATCATTTCCCGTGCGGGCGGTGCGCCGACGCTGGCGGTGGGGATGGCCTACATTCTGCACGGCGCGCTGGGCGGCATGATGGATGTGGCGTTCTGGTA                                       <  SRR3722135.196361/151‑1 (MQ=60)

                                                                                                GCATTACACCAGATACGCTAAACCAGATTGCCAGCGAAGTGGGTGAACAGCCGATCATTTCCCGTGCGGGCGGTGCGCCGACGCTGGCGGTGGGGATGGCCTACATTCTGCACGGCGCGCTGGGCGGCATGATGGATGTGGCGTTCTGGTA                                       <  SRR3722135.232305/151‑1 (MQ=60)

                                                                                                     ACACCAGATACGCTAAACCAGATTGCCAGCGAAGTGGGTGAACAGCCGATCATTTCCCGTGCGGGCGGTGCGCCGACGCTGGCGGTGGGGATGGCCTACATTCTGCACGGCGCGCTGGGCGGCATGATGGATGTGGCGTTCTGGTATCACT                                  >  SRR3722135.458424/1‑151 (MQ=60)

                                                                                                                        AGATTGCCAGCGAAGTGGGTGAACAGCCGATCATTTCCCGTGCGGGCGGTGCGCCGACGCTGGCGGTGGGGATGGCCTACATTCTGCACGGCGCGCTGGGCGGCATGATGGATGTGGCGTTCTGGTATCACTTCGCCATTTTGTTTGAAGC               <  SRR3722135.257286/151‑1 (MQ=60)

                                                                                                                                      GTGGGTGAACAGCCGATCATTTCCCGTGCGGGCGGTGCGCCGACGCTGGCGGTGGGGATGGCCTACATTCTGCACGGCGCGCTGGGCGGCATGATGGATGTGGCGTTCTGGTATCACTTCGCCATTTTGTTTGAAGCACTGTTTATTCTG  >  SRR3722135.50733/1‑150 (MQ=60)

ATTTTGCCATGAACAGCCCGATGGCGGTGCTGGCTCCGGCAGGGACGGCGGATGTGGTCGCTTCTGCCGCGCAGGTGGTGAGTAGCTGGGGCTTTAGCATTACACCAGATACGCTAAACCAGATTGCCAGCGAAGTGGGTGAACAGTCGATCATTTCCCGTGCGGGCGGTGCGCCGACGCTGGCGGTGGGGATGGCCTACATTCTGCACGGCGCGCTGGGCGGCATGATGGATGTGGCGTTCTGGTATCACTTCGCCATTTTGTTTGAAGCACTGTTTATTCTG  >  NZ_CP009273/626518‑626801

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 26 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`