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
A1 F28 I1 R1	163	52.9	1786516	99.3%	1774010	139.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,635,815	(C)_5→4	coding (33/963 nt) coding (553/570 nt)	ydfN ← nohA ←	Qin prophage; putative side tail fiber assembly protein Qin prophage; putative prophage DNA‑packaging protein NohA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,635,811	0	C	.	92.9%	102.1 / 2.8	28	coding (37/963 nt) coding (557/570 nt)	ydfN nohA	Qin prophage; putative side tail fiber assembly protein Qin prophage; putative prophage DNA‑packaging protein NohA
Reads supporting (aligned to +/- strand): ref base C (1/1); new base . (14/12); total (15/13)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.52e-01

CATGAGCACCGCTTGTACCACTCCAGCCGATGAGTAACTCACCTTCGCCAACGGCTGTCATCCCTTTCAGGTGAATGATATTTCCATACGCTGTTGGATATCCGTTGTTATACACCTCGTATAACTCAAGACCTGCTGCCCCCTGCGTATTGTCTGTCAGCGCGGTTATATTCACTCAGCAACCCCGGTATCAGTTCATCCAGCGCGGCTGCTTTGTTCATGGCTTTGATGATATCCCGTTTCAGGAAATCAACATGTCGGTTTTCCAGTTCCG  >  NC_000913/1635673‑1635946

cATGAGCACCGCTTGTACCACTCCAGCCGATGAGTAACTCACCTTCGCCAACGGCTGTCATCCCTTTCAGGTGAATGATATTTCCATACGCTGTTGGATATCCGTTGTTATACACCTCGTATAACTCAAGACCTGCTGcc                                                                                                                                        <  2:420408/140‑1 (MQ=255)

 aTGAGCACCGCTTGTACCACTCCAGCCGATGAGTAACTCACCTTCGCCAACGGCTGTCATCCCTTTCAGGTGAATGATATTTCCATACGCTGTTGGATATCCGTTGTTATACACCTCGTATAACTCAAGACCTGCTGccc                                                                                                                                       <  1:126581/140‑1 (MQ=255)

 aTGAGCACCGCTTGTACCACTCCAGCCGATGAGTAACTCACCTTCGCCAACGGCTGTCATCCCTTTCAGGTGAATGATATTTCCATACGCTGTTGGATATCCGTTGTTATACACCTCGTATAACTCAAGACCTGCTGccc                                                                                                                                       <  1:595768/140‑1 (MQ=255)

        ccGCTTGTACCCCTCCAGCCGATGAGTAACTCACCTACGCCAACGGCTGTCATCCCTTTCAGGTGAATGATATTTCCATACGCTGTTGGATATCCGTTGTTATACACCTCGTATAACTCAAGACCTGCTG‑CCCCTGCGTa                                                                                                                               <  1:381086/140‑1 (MQ=255)

        ccGCTTGTACCACTCCAGCCGATGAGTAACTCACCTTCGCCAACGGCTGTCATCCCTTTCAGGTGAATGATATTTCCATACGCTGTTGGATATCCGTTGTTATACACCTCGTATAACTCAAGACCTGCTG‑CCCCTGCGTa                                                                                                                               <  1:286353/140‑1 (MQ=255)

        ccGCTTGTACCACTCCAGCCGATGAGTAACTCACCTTCGCCAACGGCTGTCATCCCTTTCAGGTGAATGATATTTCCATACGCTGTTGGATATCCGTTGTTATACACCTCGTATAACTCAAGACCTGCTG‑CCCCTGCGTa                                                                                                                               >  1:672697/1‑140 (MQ=255)

        ccGCTTGTACCACTCCAGCCGATGAGTAACTCACCTTCGCCAACGGCTGTCATCCCTTTCAGGTGAATGATATTTCCATACGCTGTTGGATATCCGTTGTTATACACCTCGTATAACTCAAGACCTGCTG‑CCCCTGCGTa                                                                                                                               <  1:167134/140‑1 (MQ=255)

         cGCTTGTACCACTCCAGCCGATGAGTAACTCACCTTCGCCAACGGCTGTCATCCCTTTCAGGTGAATGATATTTCCGTACGCTGTTGGATATCCGTTGTTATACACCTCGTATAACTCAAGACCTGCTGCCCCC‑GCGTAt                                                                                                                              >  1:595591/1‑140 (MQ=255)

              gTACCACTCCAGCCGATGAGTAACTCACCTTCGCCAACGGCTGTCATCCCTTTCAGGTGAATGATATTTCCATACGCTGTTGGATATCCGTTGTTATACACCTCGTATAACTCAAGACCTGCTG‑CCCCTGCGTATtgtct                                                                                                                         >  2:829049/1‑140 (MQ=255)

                   aCTCCAGCCGATGAGTAACTCACCTTCGCCAACGGCTGTCATCCCTTTCAGGTGAATGATATTTCCGTACGCTGTTGGATATCCGTTGTTATACACCTCGTATAACTCAAGACCTGCTGCCCCC‑GCGTATTGTCTGTCAg                                                                                                                    <  2:595591/140‑1 (MQ=255)

                     tCCAGCCGATGAGTAACTCACCTTCGCCAACGGCTGTCATCCCTTTCAGGTGAATGATATTTCCATACGCTGTTGGATATCCGTTGTTATACACCTCGTATAACTCAAGACCTGCTG‑CCCCTGCGTATTGTCTGTCAgcg                                                                                                                  <  2:684055/140‑1 (MQ=255)

                     tCCAGCCGATGAGTAACTCACCTTCGCCAACGGCTGTCATCCCTTTCAGGTGAATGATATTTCCATACGCTGTTGGATATCCGTTGTTATACACCTCGTATAACTCAAGACCTGCTG‑CCCCTGCGTATTGTCTGTCAgcg                                                                                                                  <  2:672697/140‑1 (MQ=255)

                      ccAGCCGATGAGTAACTCACCTTCGCCAACGGCTGTCATCCCTTTCAGGTGAATGATATTTCCATACGCTGTTGGATATCCGCTGTTATACACCTCGTATAACTCAAGACCTGCTG‑CCCCTGCGTATTGTCTGTCAgcgc                                                                                                                 >  1:385738/1‑140 (MQ=255)

                       cAGCCGATGAGTAACTCACCTTCGCCAACGGCTGTCATCCCTTTCAGGTGAATGATATTTCCATACGCTGTTGGATATCCGTTGTTATACACCTCGTATAACTCAAGACCTGCTGcccctgcg                                                                                                                                  <  1:394393/123‑5 (MQ=255)

                       cAGCCGATGAGTAACTCACCTTCGCCAACGGCTGTCATCCCTTTCAGGTGAATGATATTTCCATACGCTGTTGGATATCCGTTGTTATACACCTCGTATAACTCAAGACCTGCTGcccctgcg                                                                                                                                  >  2:394393/1‑119 (MQ=255)

                         gCCGATGAGTAACTCACCTTCGCCAACGGCTGTCATCCCTTTCAGGTGAATGATATTTCCATACGCTGTTGGATATCCGTTGTTATACACCTCGTATAACTCAAGACCTGCTG‑CCCCTGCGTATTGTCTGTCAGCGCGGt                                                                                                              >  2:151254/1‑140 (MQ=255)

                                      tCACCTTCGCCAACGGCTGTCATCCCTTTCAGGTGAATGATATTTCCATACGCTGTTGGATATCCGTTGTTATACACCTCGTATAACTCAAGACCTGCTG‑CCCCTGCGTATTGTCTGTCAGCGCGGTTATATTCACTCAg                                                                                                 >  2:464107/1‑140 (MQ=255)

                                       cACCTTCGCCAACGGCTGTCATCCCTTTCAGGTGAATGATATTTCCATACGCTGTTGGATATCCGTTGTTATACACCTCGTATAACTCAAGACCTGCTG‑CCCCTGCGTATTGTCTGTCAGCGCGGTTATATTCACTCAGc                                                                                                <  1:829049/140‑1 (MQ=255)

                                        aCCTTCGCCAACGGCTGTCATCCCTTTCAGGTGAATGATATTTCCATACGCTGTTGGATATCCGTTGTTATACACCTCGTATAACTCAAGACCTGCTG‑CCCCTGCGTATTGTCTGTCAGCGCGGTTATATTCACTCAGCa                                                                                               <  1:63227/140‑1 (MQ=255)

                                                 aaCGGCTGTCATCCCTTTCAGGTGAATGATATTTCCATACGCTGTTGGATATCCGTTGTTATACACCTCGTATAACTCAAGACCTGCTG‑CCCCTGCGTATTGTCTGTCAGCGCGGTTATATTCACTCAGCAACCCCGGTa                                                                                      <  2:464764/140‑1 (MQ=255)

                                                 aaCGGCTGTCATCCCTTTCAGGTGAATGATATTTCCATACGCTGTTGGATATCCGTTGTTATACACCTCGTATAACTCAAGACCTGCTG‑CCCCTGCGTATTGTCTGTCAGCGCGGTTATATTCACTCAGCAACCCCGGTa                                                                                      <  1:151254/140‑1 (MQ=255)

                                                                   cAGGTGAATGATATTTCCATACGCTGTTGGATATCCGTTGTTATACACCTCGTATAACTCAAGACCTGCTG‑CCCCTGCGTATTGTCTGTCAGCGCGGTTATATTCACTCAGCAACCCCGGTATCAGTTCATCCAGCGCgg                                                                    >  1:374521/1‑140 (MQ=255)

                                                                        gAATGATATTTCCATACGCTGTTGGATATCCGTTGTTATACACCTCGTATAACTCAAGACCTGCTG‑CCCCTGCGTATTGTCTGTCAGCGCGGTTATATTCACTCAGCAACCCCGGTATCAGTTCATCCAGCGCGgctgct                                                               <  2:286016/140‑1 (MQ=255)

                                                                                           tGTTGGATATCCGTTGTTATACACCTCGTATAACTCAAGACCTGCTG‑CCCCTGCGTATTGTCTGTCAGCGCGGTTATATTCACTCAGCAACCCCGGTATCAGTTCATCCAGCGCGGCTGCTTTGTTCATGGCTTtgatga                                            <  2:603382/140‑1 (MQ=255)

                                                                                             ttGGATATCCGTTGTTATACACCTCGTATAACTCAAGACCTGCTG‑CCTCTGCGTATTGTCTGTCAGCGCGGTTATATTCACTCAGCAACCCCGGTATCAGTTCATCCAGCGCGGCTGCTTTGTTCATGGCTTTGATGata                                          >  1:760643/1‑140 (MQ=255)

                                                                                               ggATATCCGTTGTTATACACCTCGTATAACTCAAGACCTGCTG‑CCCCTGCGTATTGTCTGTCAGCGCGGTTATATTCACTCAGCAACCCCGGTATCAGTTCATCCAGCGCGGCTGCTTTGTTCATGGCTTTGATGATATc                                        <  2:374521/140‑1 (MQ=255)

                                                                                                     ccGTTGTTATACACCTCGTATAACTCAAGACCTGCTG‑CCCCTGCGTATTGTCTGTCAGCGCGGGTATATTCACTCAGCAACCCCGGTATCAGTTCATCCAGCGCGGCTGCTTTGTTCATGGCTTTGATGATATCCCGttt                                  >  2:839435/1‑140 (MQ=255)

                                                                                                                cacCTCGTATAACTCAAGACCTGCTG‑CCCCTGCGTATTGTCTGTCAGCGCGGTTATATTCACTCAGCAACCCCGGTATCAGTTCATCCAGCGCGGCTGCTTTGTTCATGGCTTTGATGATATCCCGTTTCAGGAAATCaa                       >  2:640631/1‑140 (MQ=255)

                                                                                                                cacCTCGTATAACTCAAGACCTGCTG‑CCCCTGCGTATTGTCTGTCAGCGCGGTTATATTCACTCAGCAACCCCGGTATCAGTTCATCCAGCGCGGCTGCTTTGTTCATGGCTTTGATGATATCCCGTTTCAGGAAATCaa                       >  2:818743/1‑140 (MQ=255)

                                                                                                                   cTCGTATAACTCAAGACCTGCTG‑CCCCTGCGTATTGTCTGTCAGCGCGGTTATATTCACTCAGCAACCCCGGTATCAGTTCATCCAGCGCGGCTGCTTTGTTCATGGCTTTGATGATATCCCGTTTCAGGAAATCAACAt                    >  2:318267/1‑140 (MQ=255)

                                                                                                                   cTCGTATAACTCAAGACCTGCTG‑CCCCTGCGTATTGTCTGTCAGCGCGGTTATATTCACTCAGCAACCCCGGTATCAGTTCATCCAGCGCGGCTGCTTTGTTCATGGCTTTGATGATATCCCGTTTCAGGAAATCAACAt                    >  1:152454/1‑140 (MQ=255)

                                                                                                                       tataACTCAAGACCTGCTG‑CCCCTGCGTATTGTCTGTCAGCGCGGTTATATTCACTCAGCAACCCCGGTATCAGTTCATCCAGCGCGGCTGCTTTGTTCATGGCTTTGATGATATCCCGTTTCAGGAAATCAACATGTCg                >  1:692587/1‑140 (MQ=255)

                                                                                                                                aGACCTGCTG‑CCCCTGCGTATTGTCTGTCAGCGCGGTTATATTCACTCAGCAACCCCGGTATCAGTTCATCCAGCGCGGCTGCTTTGTTCATGGCTTTGATGATATCCCGTTTCAGGAAATCAACATGTCGGTTTTCCAg       >  2:589175/1‑140 (MQ=255)

                                                                                                                                     tgctg‑cCCCTGCGTATTGTCTGTCAGCGCGGTTATATTCACTCAGCAACCCCGGTATCAGTTCATCCAGCGCGGCTGCTTTGTTCATGGCTTTGATGATATCCCGTTTCAGGAAATCAACATGTCGGTTTTCCAGTTCCg  <  1:818743/140‑1 (MQ=255)

CATGAGCACCGCTTGTACCACTCCAGCCGATGAGTAACTCACCTTCGCCAACGGCTGTCATCCCTTTCAGGTGAATGATATTTCCATACGCTGTTGGATATCCGTTGTTATACACCTCGTATAACTCAAGACCTGCTGCCCCCTGCGTATTGTCTGTCAGCGCGGTTATATTCACTCAGCAACCCCGGTATCAGTTCATCCAGCGCGGCTGCTTTGTTCATGGCTTTGATGATATCCCGTTTCAGGAAATCAACATGTCGGTTTTCCAGTTCCG  >  NC_000913/1635673‑1635946

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